I want to hook my brothers win98 HD to my new system as slave so i can back up whats needed to rewriter on my system, as hes having problems with his cd-rw.

Will i be able to access the win98 HD if its set to slave?

I don't see why there should be any problem.the OS is on your master, so that is in charge of things, you should be able to back up everything you need.