So I have a 2001 A4 2.8 that overheated on me back in December. I did have a misfire on it back then that kept jumping around different cylinders in both banks.

I found a used engine and replaced it the one I had with a 1998 2.8 engine (drive by cable) so I had to change quite a bit of parts over from the old one. Now I started up the car last week and it gave me a misfire and was running really rough since two of the coil wires were exchanged. After moving them over to the correct order everything was ok. I left it running for about 2 hours or more. I accelerated it and everything was ok no misfires or engine light. I took it for a drive and after 40 mph the light came on. Scanned it and it gave me an error of cylinders 4, 5, and 6. I was told that maybe resetting the throttle body might do the problem. So I did that and now it’s running even worse.

I have been playing around with it and it seems that it is only when it is running. When sitting in Park I can rev the engine past the 5500 RPM but when it gets to the 6000RPM it would start flashing.

When running the light starts flashing after 35 MPH when if I'm near the 3000RPM and continues to flash up until around 65 if I stay at a constant 70 MPH it will stop. If I continue to accelerate past the 70 MPH area it would start flashing again.

Now if I slowly accelerate to 65+, keeping RPM's under 2000 it won’t flash and will be ok.
The coil pack is new.
The spark plugs are new
Speed sensor is the one that I had bought before.
Vacuum lines have been replaced.
Breather valve is new.

Hope what I’m saying is understandable. Let me know if not.

Thanks