Hook up as much stuff as you can to the stock wiring harness. Basically, the only thing you're changing is the fuel injection. I'm not sure why you're ditching the 4L60E.....theres plenty of people that make some great built units and you can actually drive on the freeway as well. But still hook up all other possible connections i.e.- MAP sensor, coolant sensor, ignition (get an MSD box if you think you need one), brakes, knock sensor, power steering, A.C., oil pressure sensor, etc.
Theres no reason to ditch the whole entire computer! It's a benefit even when doing performance builds. Even the TBI in your truck can be modded for a stroker, just call Fastchip (who did my custom tune, and perform custom TBI tunes all day long) and tell them what you're doing. If you ditch the computer totally, and go to a carb, drivability will suffer. I could have done the same thing, but even with my crappy fuel injection I was able to make it work and benefit from all the conveniences of EFI as well.