UPDATE!!
Well I am glad to report that after getting the transmission back in, I believe the vibration is gone! I will fully confirm this when the car is out on the road (hopefully tomorrow), but before I tore it apart, I could feel the vibration with the car up on jackstands, and currently there isn't any vibration with the car still on jackstands.
Before the transmission went back in, I got to spray some undercoating on the bottom of the car, especially the transmission tunnel, which did not get done last time I applied POR-15 to the underside of the car.
Here's where the car sits now. I am in the process of getting my new tailpipes fit to the car, which came out of a buddies new-edge, so they require a little bit of work to fit just right, but should be worth it in the end.
Also, my shifter boot fell off once again, even after I tried to use hot-glue to reattach it to the plastic surround. Sooooo I decided to try something I've been thinking about for a while now, and it actually worked really well! Essentially, 'plastic soldering'. I have an attachment on the front of my snap-on soldering iron that is shaped like a blade, meant for cutting plastic. I combined that with a few zipties I had, and basically fed the zipties into the hot blade which was right next to the plastic shifter surround, and reattached the shifter boot to the surround that way. When all was said and done, it is really really stout and doesn't seem to want to separate with a decent amount of force applied to it. It may not be pretty on the underside, but it works well, and thats all that matters:
I will probably use the same method for my ebrake boot, which has also torn away from the console, even after attempting the hot glue method.
Tomorrow I hope to finish up with the tailpipe install, give the car its first wash in over 6 months, and drive the thing!
Questions/Comments welcome