Seems like you're 90% of the way there. Get your hands on a wiring diagram, and trace back to where the pre-charge unit ties into a voltage source. There's either a break in the line, a relay is bad, or (most likely) there is a connector that wasn't hooked back up when the new engine was installed.
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top of the intake and bypassed everything else. ( See picture)
Brake pedal is good now. But hope it wont cause other issues.
Still fighting with the coolant temp. Gauge stays at 12 oclock, but I get high readings, it goes up to 114 C at times, then as low as 96 C.
Heat now that hot. Not getting low coolant warning, but I may have to bleed it more. T Stat, and water pump are new.
I hope that head gasket stop leak did not clog my heater core. I replaced the heater control valve with a used one.