there are advantages to both.
if youre gonna run a SD hpop make sure you find the "******" cover pump with the 17* swash plate.look at the rear of the pump if the cover inside it doesnt have a bulge in it,dont waste your time or money.the nonhumped pump is the same as your stocker.
the 99-03 turbo will be an upgrade for you.toss a stock 94.5-97 compressor wheel in it and itll be fine.itll handle a few more PSI than your stocker without blowin the bushing out of it.IIRC the SD turbo is a ball bearing turbo where ours have a bushing.the stock turbo doesnt like more than around 26PSI where mine has seen 36PSI daily wich is why im on turbo #4.make sure you get the up pipes,collector,pedistal,spider,intercooler p[ipes and intercooler if you can afford it.dont need the spider,tubes and intercooler but might as well grab them.not sure if the stock intake spider will work on the sd turbo or not.not sure if the exhaust manifolds are different or not either but something tells me one of them is different than the 94.5-97.