I dropped in at BC for the weekend to get the guys to help me with the transmission and put in the new radius arm bushings and coil seats.
Turns out my very first assumption on the transmission vibration was correct:
I am concerned that in my attempt to install the transmission I may have pushed out or misaligned the pilot bearing (I did put in a new one).
Yup, when I installed the transmission it appears my "alignment tool" wasn't good enough and the input shaft pushed the pilot bearing into the crank.

. In any case no other damage was present, so we put it all back together after pulling out the old bearing and putting in a new one (correctly).
Upon further inspection of my suspension there were a few issues present:
I knew about the coil spring insulators, the shock mount being bent and the missing swaybar bushing were news to me. The passenger bearing also loosened up to the point that you could wobble the tire back and forth in the air.
I should also add that I was doing a sustained 75mph around all the curves and up and down hills on I-10 and TX-71 driving to Austin. Stripe did me a solid getting there in one piece.
I fully rebuilt the swaybar links (I had the bushings with me as I was planning to replace them anyway) and Kris helped me install the new radius bushings and coil spring isolators. As for the shock mount, when I went to bend it back up the threaded portion broke off. WTF? Turns out at one point in its life it had broken off before and the owner put it back on with a half ass weld. So what could I do? I finished bending the stud back up in place and did my own piss-poor weld to get the threaded portion re-attached. It made it back to Houston this way so I am calling it fixed.
I will need to replace those shocks though, they are WAY too long for this 2" lift, probably a large part of the reason the mount bent IMHO.
Stripe still has a vibration between 2000 and 2500 rpm. Not anywhere as bad as it was but it is still noticeable. Damn.