Oct 5 2015 update
Quick update.....IT'S ALIVE!
I got a little advice from people about what to prior to cranking over the LS swap and pretty much the answers were to just start it up.
Push it out of the garage, turned the key and vroom! Oil pressure jumped to about 45psi after about 3-5 seconds. The weird clunking noise is no longer there.
I didn't have much time this weekend so I only drove it back and forth a couple of times, but when I did the trans felt really really sluggish. I haven't hooked up the tcc from the swap yet, any chance that could be contributing to the sluggish trans?
Quick update Oct 12 2015:
I finally wired the TCC switch, CEL light, and the OBD2 port. Once they were live, the CEL was on. Pulled out the code reader....only 8 codes stored! All of them trans related.
After a little research, I ended up putting 12+ to the pink wire on connector on the drivers side (I believe it is called the PRNDL switch), instead of the round plug on the passenger side, so that explains a lot. Got the power switched and now it feels like a car again!
Rumor on the street is that I have to re-do our kitchen, then all my posts will be paint and body related updates.