Switching auto to manual, or just auto to auto isn't just a swap out, unless you do not mind and can run with ECM error codes. If you have to pass an auto inspection each year, the ECM has to recognize the TCM, or as with a manual the ECM doesn't look for data from a TCM, or it won't pass the inspection. Not needing an inspection and recognizing that you have an error code so you will not know if another one comes up, makes it easier to swap in the newer motors.
You have to be able to read wiring diagrams, and formulate a plan on how you are going to actually going to blend the two different wiring system together (or find someone who can).
Always get all the wiring that you can get, it is easier to dispose of it than get just a few more feet/colors. Some are rewiring their vehicles to match the newer ECM, TCM, BCM systems, and others are blending what needs to be connected. Trail Tough will convert some of the newer motors to make it almost a plug & play installation.
Increasing your HP dramatically will make it easier to run bigger tires, go faster, BREAK THINGS EASIER, and generally requires a little more diligence in what you are doing ALWAYS.