when you wire in the tach driver, run the 12v wire from just one cylinder through it, doesn't matter which cylinder, and then adjust your pulses per rev in the pcs software.
for your throttle signal, go to the APPS rsther than the TPS. what year is your truck? if it is an 03 or 04 then it is under the hood, if its an 05 then (as I'm sure you know) you'll have to go to the pedal assembly. you can grab it from the pcm if you want, but it is more of a pain in the ass to dig into those harnesses.
all you need to do to remedy the problem of the stock transmission being in the truck is to ground pin #4 in your factory transmission plug. it is a yellow wire with a dark blue stripe. doing this will make the truck think it is in park/neutral all the time. you do not need a manual transmission pcm. it doesn't matter what anyone tells you, you do N-O-T need a pcm for a manual transmission truck.
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