OK guys here is an update.
Just after I asked in this thread 'would installing an automatic' solve a bunch of problems I called my friend and confirmed if he still had the 'L99 with 6L80' that I was also considering.
Well he had it so he shipped that instead of the LS3 with the tr6060. I got it for less money and the l99 had less miles.
The engine is in awesome shape. I got a CRAZY good deal on it especially considering its got less than 50K miles.
4 days to go!!!!
Part of me hates that I took the easy way out...but Ive got to finish a bathroom remod and then new countertops in the kitchen. I actually didnt want to update this thread for a while because I (and likely others in the future) was still interested in how these problems were handled.
Seriously thanks for all the answers on this topic.
ALSO.....
I have front/rear discs but no booster. I will explore putting a can on it in the near future.
~JH