I'd go back to Win98 if I were you ,I havent heard a good thing said about Win ME yet ,its supposed to be very unstable!
Btw I thought the only issues of running a K6-3+ with an older S7 m/brd were voltage support & bios support.
Are you saying the DOS program you mentioned gets around the bios problem?
Have you got a link to the site? ,I'd be interested to read up about it.