It's been a long time since I have worked on this thread, but I wanted to give you an update on the situation.
The MAJOR issue with switching out my stock shocks for the hard tail struts was the fact that i tried to do it without taking any of the weight off the rear end of the bike by putting it up on a jack. I swapped them out one-by-one. I did it by physically lifting the rear frame rail up with one hand while I tried to put the bolt in to the final drive. It was one of the dumbest things I have ever done. (except for riding around for nearly 3 years with it stripped.) I do have some great news though. I went on a 2000 mile trip with my brother-in-laws and decided that before I go, I should put my stock shocks and seat back on. This included FINALLY getting to the root of the bolt issue in the final drive.
I put the bike up on a stand this time and removed the shocks correctly, including the stripped bolt. It turns out that while trying to tighten the bolt into the final drive (without a torque wrench. Another genius idea.) I sheared the bolt head from the threads. The good news is that I did not have to removed/re-tap the threads in the final drive. I simply had to buy a new bolt and clean out the final drive threads a little.
Lesson: Use the proper tools and equipment.
On the question of plasti-dip. I used it on everything but the motor. I used a satin finish high heat black for all of the engine covers and a VHT gloss black for the motor.
Here are some pictures of my bike now:
I did plasti-dip the wheel red. I will get pictures of that up soon.