Yes, a custom wiring harness is extremely helpful. Nelson makes and sells those, also. As for a manual transmission, sorry, can't help you there. I'd go automatic. I've been down the stick shift road and have fallen to the way side and am now spoiled. My left leg is no longer bigger around than my right one from pushing a clutch. Matter of fact, it's about to dwindle down to nothing because it's getting so lazy over there any more. No more hour long episodes sitting in traffic going on and off the clutch.

As for the driveshaft, if you switch to an automatic 4L60e you will need a driveshaft from a truck like yours with the 700r4 or 4L60. If you go 80e I think you can use your truck driveshaft but may have to get it shortened a little. The truck 5 speed driveshaft is the same as the turbo 400.