Wow, that's a lot of misfires. I would normally suggest that you look for a rather large vacuum leak, since it idles rough, yet runs out with good power. But you have smoked tested it and not found any leaks.
As you have a scanner, do this test as a confirmation.
With a hot engine at idle, check the 4 fuel trims, 2 short term and 2 long term. If any are >8%, then you likely have a vacuum leak. Rev the engine to 3,000 rpm for 30 seconds and watch the 2 short term fuel trims. If they reduce significantly, might even go negative, then its confirmed that you have a vacuum leak to find.
If that does not show up anything, carefully pull the connectors off the DME and check for any dirty gungy contacts. Sometimes oil or coolant wicks up the wires from leaking sensors, contaminate the contacts and cause misfires.
1999 2.8L Z3 Roadster,
2000 3.0L Z3 Roadster,
There is only one thing more pleasurable than working on a Z3, that's driving it top down on a fine day.
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