After much fiddling, I got the c drive and cd working. Then I decided to
reinstall win 98 SE. I got windows to boot normally and haven't
touched a thing in bios so I'm keeping my fingers crossed. I have to
reload a bunch of drivers because I got an initial bootup error about
child drivers or something like that. I just hope that reinstalling
drivers doesn't make things bad again.

Also I lost my secondary IDE after I put the cd drive back on it and
also my other HD so it must be a cable issue there.

Thanks for your suggestions.