Put the transmission in... most of the way. The engine needs to slide forward 1/4 inch. That should resolve most of the gapping issue on the intake once the engine is sitting in the proper place.
If it seems like I post a lot working on the car... I really do try getting out there a lot to get this thing done! If I don't do it, no one else will.
The 4L80e is a HEAVY transmission but the 7AT that was in there is nearly as heavy.
-Edit
I plan on using foil tape on the edges of the airbox and radiator. I have a v2 for both the crash bar and radiator... but I'm not going to worry about that until later down the road. I need to use what I have. That's the problem with learning curves, you always find better ways of doing things when you're done.