alm4rr, watch out copying files from your current HDD to a backup drive using DOS, you may lose all your long filenames. For the time it takes it might be worth installing a basic Win98 install on your spare 4 gig drive, get into windows long enough to back up the files from the 30 gig, then format and install win98 on it.
Although in reality you should be able to boot into windows from the existing install on the 30gig drive, just skip all the new hardware detected, you might only be running in 640x480 but it would be good enough to get your files copied onto the spare 4gig. If it doesn't work, no harm done your data on the 30gig will be intact and you can use the other method from above.
Another option would be to just delete (or rename) the 'windows' and 'program files' folder on your existing drive from a command prompt, and install Windows on the drive as if it was formatted. I've done this several times and it always works well. You just gotta watch that if you rename windows, the Win98 setup program will see it and try to install over top of it into that renamed windows folder, you have to specify a new folder for the install.