1-sn95 best year probably be 98, 99+ all the years are good as far as I know, I would probably look for 2000+ instead of a 99 b/c they usually have some bugs during first year of production.
2-Cost of Parts are probably about the same now. They may be slightly more but not a huge difference.
3-well for something like heads or cams it will be more. The 4.6 is alot different than the 5.0 and it can be a real PITA to rip down to install that stuff. So yed the install will definetly be more money and more time consuming.
4-5.0 better low end, 4.6 better mid and upper rpm. 96-98 specs and 5.0 specs are very similar, stock not much difference in power. Other night i raced a modified 5.0 w/ exhaust, intake, and u/d's and we were about even up to 70 then we both let off. He had me by a fender, but look at my mods, compared to what he had.
5-well biggest restriction on 96-98 4.6's is the npi intake cams and heads. But other than the all the 4.6's have restrictive air boxs and exhaust.
6-500 hp out of a 4.6.... it would be tough you would probably be better off getting a 4.6 DOHC and doing it that way. On a 4.6 sohc you would need alot of work to get to 500.
7-you asked the same question as 2
8-both are very reliable motors
9-not positive on this one but i would guess it gets better mileage. But who cares, i doubt you are buying a
stang for mileage. And once you start moding your car mileage goes out the window anyway.
10-i would stay away from any 96-98 with the plstic crossover intake, b/c it will crack. Other than that there are really no bugs i can think of. Unless you start looking into cobra's, b/c the 96-98 cobras needed a special upgrade from the factory to increase its hp to where ford rated it at. I am not sure what the upgrade consisted of but if your gonna go that route make sure you find out that info.
IMO the 4.6 is a great motor. I would say get a 4.6 since they are readily available right now, and there is now alot more mods for the 4.6 then a few years ago.