Modifications acceptable to the computer

I have a 1996 1-ton Chevy pickup (with service body full of heavy stuff); factory 350 with the new-that-year central sequential fuel injection, turning an automatic with overdrive. The engine has a hard rattle on start-up, which mostly goes away as the engine warms. I figure somebody had a coolant leak and skidded a piston. Engines can keep going for years with this, but sooner or later I suppose I'll do an overhaul . . .

. . . with improvements. At least I intend them to be. I don't want to put gobs of cash into this truck, so I don't think I'll go to the expence of making it into a 383, as much as I like that upgrade. But I want to deck the block enough to have a proper squish-height. I'll clean up the ports and bowls, match ports and manifolds, and see if somebody has found ways to enhance swirl in these already swirly heads. Yeah, I'll probably make them groovy as well. I'm hoping to get small improvements in fuel efficiency and power, on regular gas. If the squish and the grooves allow me to squeeze the compression slightly harder (that is, BEYOND the slight increase I'll get anyway from re-surfacing the heads and from decking the block to get good squish), I might chance that. Since the cam probably needs a re-grind anyway, I might go for an aftermarket RV cam or mileage cam if I hear enough raves. With all of this, I have to bear in mind the bi-annual emissions sniffs (which don't look at nitrogen oxides, thankfully).

Given all of that, what I'd like to know from this forum is how much lattitude for modification is there before the computer gets confused. And, is there a "best" GM-specific website to search for this info, both computer and engine mods.