Well, if the PC is running FAT32, and you want the external disk to be NTFS to avoid file size limit ... you shouldn't have any files on the machine that would break the limit?
But other than me being a smartass (not really because I bet you already considered that), and focusing on the idea that you want to use it in the future (where there is no such restriction), it looks like 9x Kernel (95/98/ME) needs 3rd-party support to run NTFS.
A google search of "windows ME NTFS" yields this as the first result:
http://www.sysinternals.com/Utilitie...Windows98.html
It might really not help you at all, but I'm exhausted and I need to sleep. Hope that helps!
EDIT: I like your signature by the way, it meant something to me last night :P