If you want to start fresh, make a Win98 boot floppy, and boot from the floppy drive. When you get to the A: prompt, type in format c
assuming this is the partition you want to format and install Windows to) . This will wipe out everything on your drive, so you'd better back up all of your info first.
You can speed up your Windows setup by copying the CD to your harddrive. c:md win98, c:cd win98, c:copy e:\win98\*.*\c:\win98\*.*/e(this assumes that you have one partition, and your CDROM is the E: drive. If it isn't, type DIR at each drive letter until you find your Windows CD. That is the CDROM).
Then type in setup /?. This will allow you to turn off the ads, the boot floppy, and other things.
I don't think you can install Windows without installing IE, though I guess you can uninstall it afterwards. I just ignore it.
I'm not sure about why you can't save your Winipconfig settings.