Get under your car and check the pinion angle. I had the same problem, but with a lot of tweaking and testing, I have the vibration almost gone. The angle possibly changed due to what you used part-wise. What crossmember did you run? M6 w/ spacers, or a sponser th400 LS1 swap crossmember? I used an M6 w/ 1" worth of spacers and a th400 trans mount like the stickies said and the angle deffinately didn't stay the same as it was stock. That is where I would start first. When I had that problem, someone gave me good advise. If you have access to a dyno, run it and get under there and video tape the tranny, driveshaft, and rear end. That way you can go back and slow the footage down and possibly get a good idea of what and where exactly the problem is occuring. One thing I love is when I converted everything to double adjustable stuff and adjustable TQ arm etc. best thing. It takes no time to do pinion angle. When I had to keep tweaking the adjuster a 1/4 turn each time to dial in the angle, I got to the point where I could park the car, put the back on stands, adjust it, and have the car sitting on the ground ready to go in 5 mins w/ hand tools. I would check the angle first since that is easy to do and rule out.
here is a link to a post that I did on a different message board. It is 2 pages of different things that I looked at over the course of a few weeks. Maybe something in there can give you help. It deffinately helped me..
http://www.yellowbullet.com/forum/sh...d.php?t=167059
mark jr.