Weird running after modifications, need help troubleshooting

[CombatWombat]

2001 BMW 530i LCI, m54b30
Over the winter while my car was garaged I decided to do some small projects I had wanted to do, and I did a new VCG & installed catless headers. VCG had no clear issues, doesn't seem to leak etc. Catless headers were installed fine, fairly confident is no exhuast leaks, and I fabbed a blockoff plate for the secondary air check valve. I removed & unplugged downstream 02 sensors and blocked the ports in the new headers, as they should be unnecessary since they are for monitoring cat health. Upstream sensors intact and are reading on INPA.

Had to take the car to an exhaust shop to get the exhaust flanges welded to meet up with the header flanges (because cheap ebay crap headers ) But when I was running & driving the car dumping from the headers I noticed no irregularities in how it was running. Or maybe I just couldn't hear it since it was too loud. Either way, I didnt have my computer to check INPA after driving with the header dump, but when i started it for the first time with the header dump there was no new codes from before (though that is likely because computer hadn't seen anything wrong yet). After running & driving it with the header dump, it still didnt even get a CEL.

After the exhaust was re-welded, I got a CEL and the motor was running choppy when I picked it up from the shop. I checked INPA and have the codes in the attached PDF. While looking at INPA more, I checked "rough" and it indicated cyl 1 burn quality as very far in the red. I replaced spark plugs & ignition coil, and no change. I looked around in INPA more, and found I could clear "adaption irregular running", and after that the motor ran weird, but better - and "rough" indicated that all cylinders were a little bit in the red (maybe just running rich?)

test drove, and after a couple minutes at low speeds, all values in "rough" were in the green, and after a couple more minutes at higher speeds, cylinder 2 had a very high rough value (similar to cylinder 1 before i cleared irregular running). I have looked at all of the codes, but they are difficult to find clear answers as to what (in my situation) is causing them, and I am unsure which ones are actually causing the irregular running. (also note, code 227 and 228 the car has had since i bought it, and the car has ran completely fine with those codes, so it is unlikely those are the issue)

Thank you to anyone who can help or has insight.

code history \/
e39m54errmem.pdf

[jicaino]

Did you reset adaptations? Do you know If the exhaust shop disconnected the battery before welding? They could have f'd up your o2 sensors or maybe something is tangled (wiring harness wise)

[CombatWombat]

I reset only irregular running adaptations, as well as lambda adaptations since I figured those were the most relevant. I could try resetting all though. And yes, the car actually had no battery even in it while it was at the shop. There is a chance something may be tangled, I did do a lot of twisting of the 02 sensor wires in order to get them screwed into the headers, and moved wiring around. Doubtful I did tangle wiring, but I will check today.

[jicaino]

Damn server ate a long answer
Check the actual wiring between the sensors and the e-box, then monitor sensors using inpa or something that can see live data, if both things check up fine, you knight need a tune

[CombatWombat]

Update, car still doing same thing - followed some wiring and does not seem to be messed up.
I reset all adaptations, after a couple minutes it straightened itself out and seemed ok. Drove it, all seemed well besides power dip at high revs (noticed in second gear). INPA was showing green for "rough". Was a short drive, only 5 or so minutes to get gas but nothing changed really. Got home, and the car had difficulty idling, with the same issues I had described before.
Tried removing MAF as I read in the e46 forums that some people with similar issues could correct the issue by unplugging the MAF, no success just weirder running.
INPA showed this for 02 sensor values, I am not sure exactly what all of this means but I am assuming that the values reading 99+ are the removed downstream 02 sensors?
IMG_3710.jpg
I am really very puzzled - not sure whats wrong but I feel it's something small that I am missing. Everything I am reading confirms that there should not be these issues with catless headers ( and secondary air check valve & downstream 02 sensor delete ).
The old vacuum line that was on the secondary air check valve is vented to atmosphere (just not attached to anything) could that be an issue?
Is there any other sensors or readings on INPA I should check?
Thank you for the help btw lol

[jicaino]

Update, car still doing same thing - followed some wiring and does not seem to be messed up.
I reset all adaptations, after a couple minutes it straightened itself out and seemed ok. Drove it, all seemed well besides power dip at high revs (noticed in second gear). INPA was showing green for "rough". Was a short drive, only 5 or so minutes to get gas but nothing changed really. Got home, and the car had difficulty idling, with the same issues I had described before.
Tried removing MAF as I read in the e46 forums that some people with similar issues could correct the issue by unplugging the MAF, no success just weirder running.
INPA showed this for 02 sensor values, I am not sure exactly what all of this means but I am assuming that the values reading 99+ are the removed downstream 02 sensors?
IMG_3710.jpg
I am really very puzzled - not sure whats wrong but I feel it's something small that I am missing. Everything I am reading confirms that there should not be these issues with catless headers ( and secondary air check valve & downstream 02 sensor delete ).
The old vacuum line that was on the secondary air check valve is vented to atmosphere (just not attached to anything) could that be an issue?
Is there any other sensors or readings on INPA I should check?
Thank you for the help btw lol

Yes! there's a port to be plugged in the back of the manifold, where the vac line that goes to a weird NR valve that looks like a miniature old style fuel filter and then to the secondary air valve (electronic solenoid, not the SAP valve that's bolted on the side of the head). That's quite a vac leak if you haven't plugged it.

- - - Updated - - -

Also weird that the pre-cat probes are maxed out and not the post ones... and also, make sure you didn't mix up bank 1 and bank 2 sensors.

Did you remove the post cat sensors alltogether?

[CombatWombat]

Haha, I am very inexperienced with these car things, so I apologize if any of this seems obvious - it is my first real "project" car.
Just to make sure we are referring to the same things - We are both talking about the vacuum line that attaches to this right?:
Attachment 724498
I have been calling it the secondary air check valve this whole time in case I got it that wrong -_-

And yes the post cat sensors are removed completely, they are not in the manifold & are unplugged at where they plugged into near the fuel rail. the video I was following and other peoples on the internet said they are unnecessary, as they only function to monitor cat health essentially, which is not necessary when switching to a no cats setup. or at least so i was told haha. the holes where they would be are plugged and sealed with copper crush washers

Would you know how to confirm that the 02 sensors are in the correct manifold? I am fairly certain that they're in the correct ones, but I guess just to be thorough it couldn't hurt to check.

[JimLev]

That’s not a check valve, it’s a on/off valve. The vac line that attaches to the barb goes to an electric valve that the DME turns on during cold start.
You need to plug that vac line.

[CombatWombat]

.-.
will plug line tomorrow and update if issues persist
thank you for assistance and bearing with me haha.

[jicaino]

That’s not a check valve, it’s a on/off valve. The vac line that attaches to the barb goes to an electric valve that the DME turns on during cold start.
You need to plug that vac line.

All of the SAP systems I've seen have a vac line from the manifold, plugged to a check valve, that line goes to a solenoid that has wiring to be turned on/off and that's what actuates the control valve. I was merely describing that arrangement that if you delete, you need to plug the source of manifold vac....

But if you're not understainding me maybe OP will not either. Just to disambiguate, marked with the red X it's all you deleted. You need to plug the fitting in the back of the manifold, where you removed that hose taht goes to the click valve, the on-off valve and the conttol valve of the secondary air system.
SAPdel.jpg

[CombatWombat]

AH - i see. you were saying manifold and I was thinking exhaust manifold, not intake. This is wicked helpful, I can not thank you more for taking the time to illustrate this out for my dumbass. Will do tomorrow and post an update.

[CombatWombat]

Update: Removed all vac hoses in illustration & plugged hole in intake manifold thoroughly. I did not remove the solenoid thing that the vac lines attach to because it was in a very difficult to get to position, and figured it would be fine to keep there temporarily while I tested (yes i unplugged the electrical plug as well).

Started car, same things. Runs perfect, then loses a cylinder after a couple minutes. I was monitoring the "rough" values and it seemed fine at first, but then the values for all of the cylinders would rise and go into the red a little bit, and then one cylinder would go very far into the red, losing the cylinder, but causing all the other cylinders to stabilize in the green.

I am going to remove the airbox and intake tubes and generally things in the area to check for vacuum leaks, though I feel that may not be causing the issue because I did not really tamper with anything in that area, and the car ran very well before.

Im feeling pretty defeated haha, any ideas?

[jicaino]

Update: Removed all vac hoses in illustration & plugged hole in intake manifold thoroughly. I did not remove the solenoid thing that the vac lines attach to because it was in a very difficult to get to position, and figured it would be fine to keep there temporarily while I tested (yes i unplugged the electrical plug as well).

Started car, same things. Runs perfect, then loses a cylinder after a couple minutes. I was monitoring the "rough" values and it seemed fine at first, but then the values for all of the cylinders would rise and go into the red a little bit, and then one cylinder would go very far into the red, losing the cylinder, but causing all the other cylinders to stabilize in the green.

I am going to remove the airbox and intake tubes and generally things in the area to check for vacuum leaks, though I feel that may not be causing the issue because I did not really tamper with anything in that area, and the car ran very well before.

Im feeling pretty defeated haha, any ideas?

Sorry, don't know what happened, I'd swear I typed an answer.

Lets recap for a minute. What did you do right before this started? Hopefully not a whole bunch of things at once. Whenever I face something similar I tend to go back to square one and retrace in order to see if I can pinpoint the moment when it started acting up.
Also, the cyl that's misfiring is #2? For some reason I think I suspect the exhaust seal around cyl #2 from your previous screen captures.

[CombatWombat]

Ok - Here is everything that is relevant
So, I have the car, i get catless headers & an aluminum valve cover. Headers are like supersprint reps.
The car, before modifications, runs like a dream. Has only two codes, both likely because small vacuum leak (but it runs well regardless).
Garage the car over the winter, do not start it for a couple months while I try put on the headers & valve cover.

Valve cover is good, put RTV on semi-circles, torque to spec, grounds back on, everything.

Headers, got on as tight as I could, used OEM e36 exhaust manifold gaskets, put some grey rtv on the gaskets before installation just to be thorough. on the headers, I used crush washers & a correctly sized plug to plug 2 holes where o2 sensors would have gone. Got rid of the 2 post catalytic convertor sensors, kept the 2 pre catalytic converter sensors. (note, I put the pre-cat sensors in the spot where the post cat sensors went for easier installaton. Tutorial I was following recommended it.)

Made a blockoff plate for the SAP control valve (I think?) out of aluminum. Its pretty beefy, I cnc'd it out of maybe 5-10 mm aluminum, idk it was definitely thick enough. Used RTV to seal it since i did not have the gasket on hand and was in a rush.

Started it for the first time for maybe 2 minutes just to hear it, it was dumping exhaust from the headers since the headers did not line up with the rest of the exhaust. I had to go on a trip shortly after, but maybe a month or so later I started it again to bring it to an exhaust shop - still running dumping exhaust from the headers. 7ish minute drive, up to temp, still running fine - Don't even have CEL yet.

Pick the car up from the shop with the exhaust welded to meet with the headers, connected with OEM flange gaskets. immediately notice it's running weird. On the short drive back, I was having trouble accelerating in the higher revs of 2nd gear.

Get access to INPA a couple days later, I check some of the readings on the car, the rough section seems to show the most. I start the car, and it is running fine, everything seems good. then, in the "rough" section, all the values start to go into the red. Then, after a minute of all the cylinders being in the red, one cylinder goes completely into the red, and gets shut off, and all of the other cylinders go back to operating normally. I do not know if there is another section of INPA I should be looking at, this one just seems to tell me the most. I try clearing adaptations, and it goes back to all of the cylinders operating but being a little in the red.

I test drive, and try revving it, and all of the cylinders go back to normal operating for a little bit. Eventually it starts acting weird later in the test drive again. I hear that some cars just need to adapt to the new higher flow headers, but cutting off an entire cylinder at idle seems to be a sign of a bigger problem I feel. Later, as you suggested I deleted the rest of the SAP lines. I left the solenoid little box thing connected to the car, but detached the wires and obvious vacuum lines connected to it (vac line going from intake manifold to solenoid, plug, and vac line going from solenoid to control valve).

I'm sorry for the very long response, I just want to be thorough. The problem cylinders are #1 and #2. Sometimes cylinder #1 stops working, sometimes cylinder #2, but never both. Is there a way I should test exhaust seal? Just spray soapy water on it maybe to see if it bubbles?