I think you might have misunderstood some of what you were reading. Some of that is concerning running a 4l80e in a setup that can't normally run one (carb, aftermarket efi, behind a non ls motor, attached to a baked potato)
When you get a harness made, you specify that you want to run a 4l80e. The branch of transmission sensors wires off of the main engine wiring harness. You don't need a stand alone harness group unless your running an aftermarket TCM controller (which you won't be doing). You can have a stock junkyard harness reworked from 4l6oe to 4l80e, the primary difference being an additional VSS (ISS) sensor.
Where exactly you get the ECM is up to whatever works for you. If you use car-part.com you can see what local yards near you have. If you still haven't found the engine yet, this WHOLE discussion is a moot point. If you find an engine/trans combo with the ECM (which is ideal) then it will ALL work together.
IF you end up needing to piece the setup together, then the important thing is finding an ECM from the same vehicle and setup. What I mean is; if you have a 2003 engine, then you want to find a 2003 ECM from a truck with a v8/auto. This is pretty easy to find, and will be CRUCIAL if you are running a DBW setup. DBW is simple to hook up, so long as you just get everything from a matching vehicle.
Like I said, I think your tripping over yourself just a bit. Its a ton of cool stuff, and a ton to read, but if you burn yourself out the project will just become a headache (for all of us
)
Now if you find an engine thats very very new, or want to run an oddball combo, then there is a bit more to work on...but we'll cross that bridge if we get there. Deal?