Why anyone would want to swap in a 42RLE is beyond me, but maybe I can help...
Regarding the TCM/PCM - they are HEAVILY integrated. In fact, in the 06 model, the TCM is part of the PCM.
Act under the assumption you will need to swap everything....PCM, complete wiring harness, pedal assemblies, switches, sensors, even transfer cases (input shaft length on the t-case is different between auto/manual). Keep in mind the output of crankshaft on the engine is slightly different as well (should be a pilot bearing on the manual).
Since you have both complete vehicles, it would probably be easiest to pull the whole front end off both vehicles (grill & fenders), and swap the engine/trans/t-case as one complete unit without unbolting them.