So i've had this problem since I did the a motor swap 30k miles ago.. I have a PoorMans R swap with a B16 transmission in my 97 civic. I've been trying to diagnose the problem since I've had it but to no avail..

When accelerating my car has a bad vibration pretty much only in 1st and 2nd gears..
1st it usually vibrates the whole way through the rpm range.
2nd gear it vibrates from where ever RPMs start and only up to 5-6k rpm.
3rd never really vibrates but if it does it's only up till about 3k rpm.
4 and 5 there's nothing.

Sometimes I don't feel the bag vibration in any gear..

I've changed the axles twice to new remans. from OReillys but with no change.
Wheel bearings seem good as there is no play but they have never been changed in 150k miles.
All mounts are good.
I've put the car up on a rack and drove through 1-3 gears but there was no vibration, only happens when under a load..

Only thing I can think is left is the intermediate shaft.. Maybe somehow it is bent?
Anyone got anything?

 

im kind of having the same problem. except mines jerk when i start to gas it more..does anyone know the reason?