That is an ambitious project which would turn an old truck into a modern running beast.
The BCM is usually programmed using the Tis2000 software (Windows based, sorry) and a J2534 passthrough tool. It can only program using available stock programs for existing models and options thus can't eliminate things like extra doors or accessories that are no longer being used, like the tailgate and doors.
I assume you want to keep some things like the HVAC, 4x4, ABS. I would recommend not using a truck that has traction control or Stabilitrak as they probably won't work right for the weight and characteristics of the old truck.
I'm not entirely sure how the BCM will react to the missing body stuff but as far as I know, most won't throw a light but the BCM will keep an internal body code. I don't think other systems care if the doors and rear hatch are missing or the radio is not there. Chassis codes are something else, like ABS and the 4x4 system as those do interact with each other as well as the PCM. The HVAC is probably the only one you would need to have working properly as the it tells the PCM to activate and control the compressor clutch. And speaking about the PCM, you'll need to have the PCM tuned to turn off most of the emissions control codes off and able to run without them unless you do want to keep them.
And engine choice can also play a role depending on what you want to do with the truck. The 4.2 is a good and powerful engine in its own right but performance parts choices are limited and mostly specialized custom parts. However, the 5.3, like all LS engines, has tons of parts for improving performance from mild to wild off the shelf. However it is wider and may be an issue to get it shoehorned in the old truck's engine bay. The 4.2 is longer and may prevent you from using a water pump mounted fan but with a good aluminum radiator and electric fans, you should be good. The stock radiator in the TB is incapable of cooling properly using electric fans.
It would be interesting to see this build documented here and how it goes.