Maddog4g43

I recently purchased a 1999 Audi A4 with 1.8 AEB engine, turns out I diagnosed the check engine light that was on real quickly, simply being the car is a 5 speed and the ECM that was in it was for and automatic, I tried recoding the ecm but codes would not take in vagcom, so I spent 40 dollars on a used 5 speed one for the same engine, and year. Took out the old one right after driving home from work put the new one in, took for a test drive, and got a jerk, hesitation, loss of power while maintaining constant speed, no cel, plugged in scanner, and had soft codes for random multiple cylinder misfires. Any idea what would cause this, car doesn't do this with the automatic ecm.