Ok I'm planning on getting a 99-00 GT as a second car but I was gonna get one with somewhat high miles and eventually get a crate engine. My question is what reasonably priced crate engines can fit the 99-03 GT without any mods? Keep in mind I know nothing about Mustangs.
As a second car - you mean as a built up "race-car"? In that case, contact MMR or VT for some good forged shortblocks. Port some PI heads, get some cams, bolt on a s/c, do some suspension, etc...