don't bother with shorty headers, longtubes with a nice x-pipe crossover with magnaflo cats into a borla/dynomax/magnaflo muffler is the way to go for exhaust.
I replaced the top end of my tahoe w/ the 5.7L vortec recently because of a cracked head and was looking into cheap mods to do at the same time, and ended up doing none of them.
the lt4 cam requires machine work to the valve seats to fit higher rated springs, the stock heads can't easily swap valve springs. Higher ratio rockers can't be swapped on either, even 1.6's are too much for the stock valve springs.
The only intake "upgrade" compatible with the stock computer is the marine vortec intake which is damn near impossible to find. 2 of the injector tubes on the stock spider of my truck were totally clogged, so I did the MPFI upgrade.
IMO, $3500 should be enough to get a motor out of a 99+ truck and swap it in, a nice 6.0L and 4l80e would be a much better way to spend your money, and they are much easier to mod later on.