Ian,
As someone who has been in the automotive business since the '70s, maybe I can help you analyze the situation.
1)Did you have the problem prior to the trans swap ?? If so, then tires,tire balance, wheel bearings,axle bearings or carrier bearings. It could even be an out of balance rear brake drum(if not 4 wheel disks).
2) If problem is since swap, then we have more possibilities. Was the trans new ?? If used, it could be the output shaft bearing in the tailpiece.However, this would usually cause a leak at that seal. It could be improper indexing of the driveshaft during installation. Did they install new u-joints ? I hope so, and I hope they used x-tra heavy duty ones. It could be a change in driveshaft angle caused by installing the new trans. If it isn't mounted at the same angle as the old tranny, this can cause problems. Either the trans mount will have to be changed/modified or you will need to change the angle that the differential "looks" at the driveshaft with shims. Another possibility is that they didn't weld the shaft back together concentricly. Was the shaft dynamically balanced after they fabricated it?If not, I suggest you take it to a high performance shop that specializes in driveshafts.
If you answer the above questions, I can reply with more suggestions.
bowhuntr