8.1L Vortec/Allison 5sp install into 56 Ford Victoria (info Needed)

I am helping my Father in-law to install a 2002 8.1L Vortec along with an Allison 1000 5sp auto into his 56 Ford Victoria car. We are in the preliminary planning stage and I am trying to round up info as he is computer illiterate. We have a complete engine and transmission with accessories and most sensors. It looks like we are only missing a MAF and both the engine computer and Allison TCM. We are missing the engine & transmission harnesses as well as we will need a TAC throttle pedal. I am looking for a little direction to track down some of these parts. So far I have found street and performance has the harnesses and I have found the ECM for $120 and the TCM for $400 at Rock auto. I am considering purchasing EFI live V2 programing to do the programming as it seems to have programming for both the engine and the Allison as well as I can use it to program my 4.8L LR4 in my Jeep project. Are there any issues with programming retrofit late model engines in old cars? What do you do with assigning Vin numbers for programing? We are planning to add a comp 270HR cam as well as run long tube headers and a good cold air intake system for engine upgrades. Does anyone have any better suggestions or direction on these parts or how to go about the install? Any info would be helpful. Thanks.
Greg