Strange Vibration after a Substantial Amount of Work

So I drove my Tacoma on the highway for the first time today after getting a good bit of work done. I haven't been driving my truck much recently, and I had some work done about 3 months ago.

I was having some bad knocking while turning, so I took my truck to the shop - it was the wheels bearings. I was at 67k, so it's just the right time for that one. I guess I left it a little long, because I also ended up with new pads and rotors. I was feeling some shimmy in the wheel under heavy braking, but figured everything maybe just needed to seat itself.

After a while, I started hearing some very strange chirping noises when going over smaller bumps. After being in the shop for a week or so, and going through quite a bit, my mechanic found that my Adjustable Bilstein 5100s had been installed incorrectly, and the top gasket had moved, causing some strange wear on the top of the shock. I had him replace those, leaving the lift at the same height (1.5").

Since I've gotten it back, the chirp is gone, but I have some HUGE vibration in the seat. I can really feel it in my stomach, to the point where it's almost unbearable. Seems to happen anywhere from 20MPH to 80MPH. I stopped by discount tire and had them rotate and rebalance the tires - that did nothing. I also noticed that under heavy breaking (80MPH->40MPH), the steering wheel now really goes crazy. The alignment also seems pretty far off - it pulls hard to the right pretty quickly.

My plan was to take it back to the shop tomorrow and get the alignment fixed, as they were supposed to do that the first time around. Could that be causing all of my problems? I'm thinking its not an engine issue, as I can't feel anything at idle or while revving in neutral. I have a little play in my driveshaft at the center bearing, but I was told that was pretty normal. Didn't have the vibration with my previous lift setting, so I can't imagine I changed the angle now.

Any thoughts on what could be causing my problem? Do the Bilsteins have a break in period? Right now I can either feel every tiny bump in the road, or it's just a low frequency vibration. Any help would be greatly appreciated!!

 

If you feel a vibration in your seat it may be the center bearing but I could be wrong. Lube the driveshaft u-joints, too. Sounds like the alignment is f'd.

 

Yeah, I'm hoping its not the center bearing, and it seems strange that it would go out at the same time as everything else. My hope right now is that it's just a big time alignment issue.