It's not the only way, but it's how I do it. Sometimes those little clips can be a pain, they're easier to get to with the motor out.
You won't normally get a harness with a domestic long block. I don't know about JDM motors.
Yeah, I have decided to do what you recommended and simply disconnect the harness at the ECU.
So I have most of what I need disconnected from the top of the engine and now comes the pain of disconnecting things while lying under the engine with engine oil dripping on my face.
Under the truck, where I would jack the transmission up seems to be blocked by some bars etc. Should I be taking these off to make sure the tranny is secured. Should I be worried about the tranny falling on my head?