Hi there, I have recently purchased a 2000 audi a4 b5 1.8T that has had an engine swap and currently has an 1999 AEB 1.8T engine in it. It appears that the previous owner who did the motor swap kept the original ecu (8D0 907 557 P) and wiring harnesses from the original engine, and I'm pretty sure they are not compatible. Since the AEB engine has less components than the ATW (the engine that originally came with the car), so there are three wires that do not connect to anything, for example, the AEB engine doesn't have a secondary air injector, so the plug in and wires just lay in the engine bay. I have had a reoccurring problem that feels almost like a misfire. It only happens when i floor the gas, like under full boost. It also only appears to happen when I am trying to pick up speed quickly by using the turbo. It progressively leads up to what feels like a misfire, and you can almost feel it coming before it happens, like lack of power. It feels like the engine surges and starts to feel like an automatic rifle under the hood until I let go of the gas.

Checked codes:
P1422- secondary air injector (this code is on because the engine doesn't have the air injector to plug the sensor into)
P1287-Turbocharger bypass valve open

I have replaced:
the PCV
Multiple check valves
Spark plugs
Pressure Regulating Valve

I have checked:
MAF sensor (tested to see if it reacts to change in rpms, and did)

Need to check still:
Fuel filter

I'm not sure what to check next besides changing the fuel filter. I do have a boost gauge and it likes to stay in the 10-15 in the vacuum side until the turbo kicks in, and it runs about 6 psi consistently. And the car feels as though it runs a ton better when cold, but once it gets toasty, it likes to do that misfire thing if I try to get on it.

Thank you for the help