Just off the top of my head, vats, shouldn't keep you from cranking, just prevent firing up?
Maybe some can correct me if I'm wrong on that.

It sounds to me like something isn't wired correctly, on a 93 truck you should be able to crank from the key without a PCM even being installed, if you jump the starter with a hand switch, does it fire up?

I would use the stock file and use vats delete patch from universal Patcher for the vats.