#1 Yes you can put a regular cable driven throttle body on that intake.

#2 You didn't get the harness with your computer and engine? I would use the stock harness and save your money. But if you want a reworked harness. I believe Allen makes them. I could be wrong???

#3 Ah... yes you will have to at least get the VATS system turned off. If you're doing that you should get a performance tune for it and remove all emissions garbage. As to who to send it to??? This is Allen's site, he's the best in my opinion and a great guy to work with. Well worth the money.

#4 I believe you're going to have to get a *bin file loaded into your PCM from a work style truck with a stick shift. You're stock PCM won't work correctly with a manual tranny behind it. On the VSS ... you'll have to check the pulses per minute from the older one and the PPM for the newer ones. I think the newer ones have a higher PPM so you'll have to get a newer one to fit.

P.S. most of the swap info for these motors have already been covered. If you check out some posts you'll find a load of info.