Sorry I was answering for the PCM only (power train control) harness wires.. looks like your pic is the total body harness. Things like ignition to starter, horn, HVAC blower motors, lights, oil, fuel temp gauges and lots more. What you are doing will require a custom body harness. Eg the starter solenoid circuit would have to be from whatever ignition switch you have, to whatever neutral safety switch you use, to the starter solenoid. That has to be repeated for everything like horn, head lights, turn signals, brake lights, HVAC blowers, AC, etc.. almost all those runs will be a custom routing in this situation.
To ans some questions.
1- The fuel pump does not provide any feedback to the PCM, since you will be activating the pump outside the PCM then that circuit is not used. BUT the PCM kills the pump if engine stops (AKA: an accident) as a safety precaution. Tieng it directly to key keeps it running in that situation, older cars used an oil pressure switch as a safety cut off.
2- The two black ground wires to PCM are spliced together in the harness there is only 1 round terminal black wire on that stud.
3- Even though you are activating the FP externally, the PCM looks for a square wave on 'Fuel Enable line" , if not there the injectors will not pick. This injector disable can be tuned out (VAT's disabled) or your Viper would have to supply the signal. Not knowing the system I can't answer if it's supplied from the Viper. E-Bay sells VAT's bypass systems that generate a signal that can be sent to the PCM, you're going to need a tune any way so just tune it out.
4- You will need one or possible two fuse boxes somewhere for the 20-30 fuses (depending on how you design power distribution) needed for the electrical system. Placement should be where it will remain dry w/convenient access with shortest wire runs. Under the hood is usually the easiest to wire and access.
I'm Bob.. 1994 Z28, A4, Stall, CAI, Cam, RR's, 342 rear, LT's , CatBack, Tuned