remove VATS: you could buy HP Tuners for about $400 plus unlock your ECU serial number for another $100 then do whatever tuning you want to it.
Those prices are about 4 years old. Luckily for me that is when one of my sons took an interest, bought it and figured it out. Now I just need to buy the ECU license and ask him to do it
So if you want to be proficient in the LS world buy that. If you just need to delete vats (and the 2nd set of O2s?) maybe cheaper to just have someone do it.
If you are on a budget there is not much you need to buy to get an LS into your old truck. Donor engine, ECU, harness, fuse box, gas pedal if it is DBC, grab the O2s if you are not going to use the stock manifolds. A tank with an in tank pump. Stuff all that in, delete VATS, run power and grounds and your good to go.
if you want neater, you either spend the time to prune the harness and change to a 4-5 fuse panel with a couple relays or you pay for after market harness. if you go the ebay harness route, pay attention to the reviews about things being wired wrong, treat it like a kit and go through every wire and connection. Both above options require understanding how LS are wired, but all the information is on the web if you look. Or pay the price to buy a name brand harness with post sales support.