The check engine light would definately come on if a cylinder was misfiring...

 

yea the torque converter sounds like thats whats wrong with it, it goes away soon as i hit the gas and on the freeways it has a slight jerk as a drive along, nothing like its missing as i drive down the road.

 

Did you check the motor mounts as Patrick suggested? alot of that sounds like it could be bad mounts. I'd hate to see you undertake a torque converter change when it could be something much more simple and inexpensive.

 

Another thought. Just to make sure you know what you are looking for, the stock mounts are made of rubber with a metal bushing in the center where the bolts run through. It is not uncommon for these monts to dryrot, or tear loose at the bushing. Push on the rubber all over the mount because the tear is not always obvious. When you get on the throttle under a load (in gear) the torque effect from the engine will cause the engine to roll towards the front or rear(depending on your engine's rotation, usually towards the rear) causing a thump or a jerk during acceleration. As for the missing, I think you guys are on the right track.