yeah let me know what happens when you swap out tranny. I talked to a mechanic at ss imports he said they had a type r in there with the same vibration problem that seemed to go away everytime he brought it to the shop. finally they opened up the differential case and there were teeth missing all over the place and that was the cause of the vibration. However…i was driving last night and it seems like when i make a sharp right turn the vibration tends to go away and when i turn left…its definitely there. I suppose ill have to start with the cheapest solution first so i guess ill replace the intermediate shaft and axles again!..might have to wait til after christmas though 
Shaking is history…thank the Lord - and some OEM remans
Ok, after a “new” set of OEM reman’d axles, a flatbedded tow back to the shop due to a worn C clip that spat the tranny axle out, and a replacement of said clip with a new one, the problem has vanished thus far. Tranny is smooth and up until now it is working fine. I’m not sure if it’s psychological and I’m over-sensitive to the most minimal shake or if the continuous shaking for 3+months caused damage to the differential, but an almost invisible 2second shake does manifest every now and then on 40 when torque is applied, but if I’m on the phone, I will have missed - this, I can live with.
Bottom line, for those of you suffering from “the shakes” when accelerating, get your axles looked at, then engine mounts - if problem persists, it may very well be that the differential has sustained moderate to heavy damage and will need to open up that tranny to fix. Otherwise, it’s just a matter of time before it grinds everything else in there to a mush and it’ll be that night when you’re with that hottie tryin to impress her with your ride @ make-out point in the middle of boondock country w/out your gun and no cell charge. Don’t get owned by Murphy and his laws, get them replaced.
Good luck guys - and thanx for all your input.
:whew:
Darn… got the same thing after installing new drive shafts 
I’m getting a vibration under acceleration and it goes away when I let off the gas. I’m going to try some of these suggestions and report back if I find out what it is. Hopefully it’s something easy to find and fix.
This is a good thread to read up on. I also am having the same issue as well and leaning towards the axles.
check your rims, maybe its out of round.