Done.

I ended up lifting 3 inches. The rear sits about 3/4 inch higher than the front. Not as high as I had it before, it was completely level. My ride isn't as stiff as before, I kind if miss the bone jarring bumps.
I ended up not indexing the passenger side. I still have about 2/3 of the nut with threads. I think it will be fine, but if I need to, I can. (the nut is like 1.5" long)
The clacking went away as well. Once the CVs were level, no problems. My CVs are now just out of level, much better than the ridiculous angle they were before the drop. I would have to work pretty hard to break one now.

The pin seems looser now that I have the truck leveled out. Still haven't pulled it. Now I have to make my new crossmember, or mod the existing one. Then the worst thing ever, clean out the garage. It is so bad right now that it isn't even usable.

On a side note, I don't think lowering the VX via torsion bars would be a good idea. It would ride like garbage. Way to soft.