It helps to:

Take pics of both engines, before yanking the old one out, to see what ran from where

Put the engines side by side on engine stands, and do a connection by connection comparison...for example, I had a few more connections hanging off the '03 engine than the '01 had.

Swap the parts on the old one onto those missing from the new one (Used engine, some paerts had been sold off by the yard already, etc...)

If you do it one at a time, methodically, one for one, its harder to lose track of what a harness was for/went to, etc.

Have help from people who actually KNOW what those pesky hoses and wires are SUPPOSED to do, so you can find the equivalent version on the other engine, as they move them around from time to time.