I have researched this for months and have actually disassembled many harnesses as well as many hours looking through wiring schematics and have written my own schematics to disassemble and reassemble factory 04/05 truck harnesses. My research has shown that using the nag1, though not impossible, is very difficult as it requires using the wheel speed sensors as well as using the body modules to shift. The easiest conversion is using a 545rfe, a small block 727, or a manual transmission and to use the 04-08 car or truck harness. The 05 truck ECM is easy to program and would control the 545rfe, or the transmission controls can be disabled to run a 727 or manual transmission. There is some good information on another site that includes my schematic for a fuse block as well as the pinouts that are needed to be retained. If you need that website pm me as I will not give that info openly without a mods permission. In plain English using the nag1 requires Hotwire's harness, programming and assistance which does not coincide with the "using your own harness" as you asked.
