Once you get Win98SE up and running, here's a couple of registry hacks that greatly improve things -
http://[url]http://www.mindspring.com/~steel_rat/Registry/[/url]
Remember how Win95 used to create columns of Programs from the Start Menu? For some reason Win98 makes you scroll up and down instead. I hate that. But "menuscroll.reg" will fix it.
The other one - "maxcashe.reg" - creates 3 more levels of system and disk cashe that will speed up your system dramatically!!! (If you don't like it, you can always change the setting back under My Computer/Properties/Performance/File System.)
If you're worried what's in these, they're just text files so open them with Notepad and you can see what I'm doing. Double-clicking will add them to your registry. You may have to right-click on them and select "Save target as..." to save them on your disk.
Also, it sounds like you had to go through the usual hoops in order get CD-ROM support. Here's a Win98SE bootdisk I put together that will autodetect your CD-ROM drive as R:
http://[url]http://www.mindspring.com/~steel_rat/win98se_boot.exe[/url]