Well guys, I think I found the issue...
A few days ago, I spent almost 2 hours road testing the car in various situations. Accel, decel, coast, clutch in, clutch out, etc, etc... I was going to swap the spare driveshaft to see if that would fix it but I found a big dent in it, so that was a no-go. I checked the pinion angle and found it was OK. I don't have adjustable control arms BTW, just econo UPR upper and lowers. All the bushings looked OK as well. I bought an FRPP aluminum driveshaft and swapped the stock driveshaft out. I found the u-joint on the yoke end had some play and it had a bad "sticky" spot when moving it around. I also had the tires balanced and removed the wheel spacers, just to be sure. I don't know if it was one single issue or a combination of them all, but the car drives amazing now. Absolutely zero vibration from 0 to 90 MPH. It feels great to drive. I was making up reasons to myself to drive around today, just so I could get out and actually drive my car for once.
And then it happened...
I got that amazing feeling of actually enjoying driving my car. That hasn't happened since 2006 when I had my Cobra. Rowing trough the gears, hearing the exhaust bellow out that sweet pushrod V8 music. I must have looked retarded because I had a stupid grin on my face the whole time I was behind the wheel. A couple of weeks ago I replaced the Pro 5.0 shifter handle with a Kona Racing titanium handle and the cheap Bullitt knockoff knob with a Fatknob. That made a huge difference. You know that point where all the small irritating issues fall away and you reach pure driving zen? When you pray that stoplight will turn red just so you can row through the gears again? Amazing. I forgot the feeling a Mustang can give you....
Even though it was a trivial issue that haunted me for awhile, I just want to thank you guys who offered all the advice. And to think I was going to sell my Mustang...