I would do two things,
First, tell the stealer to refund your money since the bike is under warranty still. You should not have had to pay, especially if they fouind incorrectly torqued bolts.
Second, go to another dealer and have them check it out. It sound like something in the drive train is out of kilter still - chain/wheel alignment in rear, front wheel, bad front sprocket, bad chain, kink/stuck links in the chain?
Now, these bikes do vibrate a bit, but it's no worse than any other vertical twin I have ridden.
Another thing I rememeber, about 2 years ago, someone had theirs checked out and it turned out that the cams were actually installed incorrectly and were off by a tooth either in the intake or exhaust, sorry I don't rememeber.
This may not have anything to do with it, but I'm grasping at straws here without actually feeling it myself.
Good luck.
If you don't get any satisfaction, give Triumph in Newnan (T of North America) a shout, maybe they will intervene and get it sorted out.
