I used to use PAF 2.0 (and even an earlier dinosaur version for an old Apple IIe which didn't even have a hard drive).I once received a GEDCOM file from someone who used a MAC and I was able to convert it to my PAF 2.0 (I believe I was running Windows 3.1 at the time.It worked well and I didn't lose any data . . . even the notes stayed intact as well as the rest of the data for about 1,500 individuals.
Now, after being away from genealogy for about five years I just downloaded PAF 4.0.1 and I'm still trying to learn how to use it. If it still accepts GEDCOM files (It must!) then I suspect that that is the way for you to go.Just preserve your 4,000 names on a GEDCOM floppy disk and then transfer them to the Windows 98 version of the upgraded PAF.