first off if you need a new stem for longer reach you need to think about that, how long is the current stem, and how long of a stem do you need. If you need a way long stem than the bike is the wrong size, get a new one.

next what kinda riding do you wanna do, if you wanna get into real mtn biking you will prolly find compatability issues with the stuff you want.

if you think your gonna make a 99 rockhopper into a remotely competative or "good" bike think again. But if all you want is somthin to ride around on fun exersize ect nothin serious than ok you could make the bike work

Price is another thing to consider, don't throw hundreds of dollars into an old bike like that, you can get a allright new bike for around $600 (give or take depending on your standards)