If you're not running a MAF then are you planning on running a Speed Density setup? Without the MAF, it's gonna run like a dog(<--strictly my opinion). The 5.3 from my donor ran real rich without the MAF attached to the throttle body before I pulled the motor.
I think you will need to have the computer tuned anyway. VATS will need to be removed for sure (or is there some other way to bypass it?). I haven't gotten to that point on mine yet but I intend to use the 4l60e and a different gear ratio than what the computer was originally programmed for so I will definitely have my tuned/reprogrammed.
Just throwing this stuff out there for you to think about. I am by no means real knowledgeable on this type of swap, but I will be before it's done!
