I think if you want EFI, A/C, and overdrive, then look at the 6.1L Gen3. I just got a 6.1 with the 5-speed auto with all the accessories and stock computer for $4,000. Getting the computer reflashed and engine wiring harness does not seem to be a problem, just more $$$. The NAG1 5-speed seems to be harder to get hooked up? A manual trans might be easier and cheaper than the auto trans?
The 6.4 Gen3 seems to still be very expensive, and the 5.7s are avaliable cheap, but don't have the upgraded components of the 6.1.