I have recently experienced a lot of problems with my LT1. I had some huge veibrations that i think i have fixed but now it still doesnt feel right. I have a new balancer and clutch set. It has brand new Iriduim plugs with OVC wires. Opti is to be believed to be original. The car vibrates and feels rough in the lower RPM's under load. When it is around 2000 - 4000 it feels rough and vibrates through the shifter and you can feel it in the car. Once in the higher RPM's it smooths out rather fine. No miss and it idles fine. Vacum lines appear fine and i wouldnt think it would be a bad plug and i know the wires arent arcing. My thoughts would be O2 sensor, fouled plug, bad motor mounts, bad opti, or something else seriously wrong. It pulls a 154 and 155 code which is O2 sensor related. Please Help!!!!!!!!

 

Since you stated the car is throwing codes, start there. I didn't see you mention the tranny mount, broken tranny mounts usually give you a thud on shifts but it's a common failure part on A4 cars.