i love the 4.6 modulars... with a simeple headswap you will see morehp and torque than the 99+ gt stangs.. the 5.0s do have more mods available, but i love the 4.6 and wouild never swap it out for anything.
It depends how much money you're willing to spend, and how much time you're willing to invest in mod'ing a motor. If you're only thinking of doing bolt-on's, with a head swap being the most invasive mod, I'd say go with a 4.6. It'll make more HP than a 5.0 with similar specs. But if you're gonna go all out, I'd say go with the '95 and build some outragous stroker. Like a 347, or a 427. With a 427, you should be able to see 400rwhp easily in N/A trim.
You will get more horsepower with the 5.0 out of the modifications you listed because the 96-98 GT's have poor flowing heads and intake manifold. If you put the heads and intake of the 99+ GT's on a 96-98 and then do those mods, you will get more power out of the 4.6.
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2008 Toyota Tacoma Prerunner SR5 Reg Cab
2.7 4 banger
No mods (yet...)
5.0 definately, easier to mod and cheaper, not to mention SIMPLER.
It is not just the cost of the parts, some installs on 4.6s are a bit more complex compared to a 5.0.
Also the 5.0 engine is pretty common in other Fords so i bet you will have less problems with the local technicians. Not many will be up to the task to touch a 4.6.
Performance wise both are similar, and will get similar results from a HEAD,CAM and INTAKE swap, more less 300HP.