Can a short block (vortec 350 with rear distributor) from a 1999 be used with the TPI setup and if so are there any alterations?

Yes, the blocks are the same.

One other question, I see my intake is using 6 bolts (per side) but the 1999 Vortec engine uses 4 (per side), am I over looking something?

nope, thats how the L31s mount. you are going to need the SDPC intake. many have redrilled the heads, but their tall intake runners create a port mismatch.

That doesn't matter if you're only interested in the short block.