Hey Chandler,
I was worried about the wiring too. I had a problem w/ different year harness's that plugged in but did not work.
I had a new FMS computer harness - bought w/ the pallet donor - It has a great manual noting how to connect the harness w/ the outside world
I had to replace the engine harness ( that's the one that runs the injectors) - $200 or so from Five Star Ford
I had the donor main harness (the massive wire mess w/ fuse box) Scared me to death, so I bought a Painless harness
I figured that I had nothing to loose stripping the donor harness as I could always use the Painless harness if I got in trouble.
Well I started ripping wires out and before I knew it I had only about a dozen wires and the thing still runs! No Painless harness needed here!
I still have the unused Painless harness if you are interested buying it.
The Painless harness is nice, but did not come w/ relays (even for the fuel pump) - I replaced all of the donor relays anyway.
Hope this helps,
Tom