Boy, that clears up a lot of things. Since Overkill Will tuned the engine in the other car then yea, it's probably something wrong with your most recent changes. You're lucky to have him as a friend. So I guess Will started with a LS6 MAF table and tuned from there?
An exhaust leak anywhere before the upstream O2 may cause what you're seeing. Did you pull the manifolds when you did the swap? You may be on the right track here.
Another thing that may be a clue that you mentioned earlier is unplugging the MAF. When you unplug the MAF the control should switch over to SD and the trim should go a little rich; not lean. This would indicate a large vacuum leak. Are you sure the IAC is working? This would also cause what you're seeing.
What about the coolant ports for the throttle body? Did you plug them? I would if you haven't already.
Lastly, did you try a new MAP sensor yet? I see your PCV catch can system is run off the original MAP sensor location? Where did you put the MAP sensor?
