Besides the saleen/eaton blower there are no actual internal mods. Saleen did manage to create a nifty aluminum intake to replace the stock composite piece. There are also 30 lbs injectors. There is the saleen water-to something intercooler, but besides that there were no major mods done to the engine. The gears were most likely the 3.08 still that year. Since that has changed to optional 3.55 i believe. The suspension was either the racecraft, which mine came with, or the saleen n2o's (?). Which are very similar to bilstiens. There are the saleen lowering springs, and the relatively large sway bars front and rear. Not sure if the control arms are modified.
It also came standard with borlas back then but no other exhaust mods, now you can get saleen x-pipes, but back then it was stock h pipe. The factory air box was also retained on the supercharged models. Not sure, but saleen may also add the differential cover, it appears that mine has it, not sure of that was factory though. Lastly, the brakes were standard Gt, unless the saleen/alcon/brembo whatever they use now was ordered. Some blown cars also came with the GOOD recaros, and Carbon Fiber heat extractor hood.
I am sure there is more, but 99 and 2000 were not as wild with the options as they are these days, but other here will elaborate on what I have said.