No questions on the modern swap yet. I'll try to stay ahead of that.
Prior to plucking the engine and trans from the donor pickup truck:
We used HP tuner software to interface with the engine and transmission module through the diagnostics port. We deleted the VATS (vehicle anti theft), deleted egr, evap, air pump, downstream cats, AC etc. everything we didn't need, we zapped. We remapped fuel mixture for a little more power in the mid to upper RPMs. We programmed the trans settings so the trans thinks it's always in "tow/haul" and we programmed for the drive sprocket vs vehicle tire size.
I then purchased a stand alone wiring harness for cleaner "engine only" wiring.
