Well I guess this thread is going to turn into my build thread. So far I think I have fixed the sunroof by locating the drain holes underneath the truck and using a compressor to blow out all the debris. Right now it seems as though I have good drainage going. Also added just a bit of 3M Sealant to a small gap in the rubber sunroof seal. I have a little bit of squeaking going on with my bouncy seats, I put some spray-on lube to the pivot points to no avail so far and will investigate further this week.
In addition, I was happy to discover receipts that show the water pump and timing belt were both replaced less than 25,000 miles ago, in fact, all the belts, hoses, plugs and plug wires were all somewhat recently replaced. Goodyear Wranglers that have less than 5000 miles on them as well. I will need a new spare, the one on it has signs of dry rot and has no air in it right now.
I forgot to add this picture in with my travel from Ft Wayne.