Whenever you want to install some app that you don't trust, run regedit, export (save) your registry and install the application. If something goes wrong, you can easily replace new registry with old one. Scanreg thing... It's hardly going to repare anything, build by M$, it is just going to destroy your system more

I'm overreacting maybe, but probability for this scenatio to happen is high

Good tools for fixing win registry, and for everything else is Norton Utilities packet, just make sure it's for w98. When w2K came out, I installed NU for win 95/98NT4 on it and after fixing stuff, during first reboot I got blue screen of death. So, make sure NU supports your w98.
regards,
levelLORD