Have Vortech V3, Don't Have Knowledge??

Welcome Uncle Matt! Looks like you got yourself a fun ride! I too have an '88 vert.
After looking at your current list of mods and supporting mods most everything looks like it will work with the V3sci.
Your 306 with those heads, intake, and assuming stock cam is probably making approx 285-300 rear wheel horsepower naturally aspirated. Add the V3sci with stock pulleys, 5psi @ 15rwhp per pound of boost is approx is 65rwhp. That puts you in the range of 350-370 to the wheels.
Using the AOD your numbers are in reality slightly less .

-At that hp range you are at the top end of the scale with the 24lb injectors. "Not good" I recommend upgrading to 42's to be safe and that will also give you growing room up to around 500rwhp.
You also mentioned stock fuel pump in your list. That definitely needs to be replaced. I would use no less than a Walbro high pressure 255lph intank. No external pump is needed.
I would also add a Kirban adjustable fuel pressure regulator to the fuel rail. Your tuner will use that for basic tuning.

As for tuning software, no software is "really" needed because most reputable tuners can tune your combo "old school" safely with timing on the distributor and the adjustable fuel pressure regulator on the rail.
However, although that is possible I like to use an SCT chip. My tuner programs my chip with my car strapped on the dyno. With that chip added to the stock computer it can and will run like a new car.
What ever you do after its all done take it and put it on a dyno at a reputable shop near you and have the air/fuel ratio checked and tuned.

Good Luck!