Don't start trying to swap computers and harnesses around (they're not even the same type of computer protocol) when it isn't necessary and you will hate yourself for it lol. Take the 06 engine, drop in 03 truck (same transmission, 545RFE; if your 03 trans is good, keep it in the truck, this will save you from having to get a quick learn at the dealer, plus not needing the extra steps). You can either swap intake manifolds or block the EGR on the 06 intake (might wanna do this since you don't know what kind of crap could have gotten into the intake from the carnage), as the 03 doesn't use EGR. Swap your valve covers and coils or get the pigtail adapters and you can keep them. There will be differences on some of the plugs, use sensors designed for the 03, not the 06. You'll also need to swap your original throttle body over as it is has a different plug than the 06. As long as you are leaving the engine stock, you don't need to change the lifters nor pull the MDS solenoids (assuming the 06 is a 1500); 03 doesn't have MDS. As long as you leave the solenoids IN and unplugged (you won't have a harness from the 03 truck anyway) the default position for MDS is off until activated. Since nothing will ever activate it, the engine will act like normal always running on all eight cylinders. Do NOT pull the solenoids if you are leaving the lifters in, as the MDS specific cylinder lifters will collapse and you will have a large displacement four cylinder.
