I'm wondering if maybe looking at it from the other end might help...
I found a page at Frank Condron's World O' Windows (sorry, I don't have the URL handy) that describes how to remove Win 2k from a dual boot setup, and it said to remove these files (in addition to the \winnt directory):
ntldr
ntdetect.com
boot.ini
pagefile.sys
bootsect.dos
So I'm wondering if those are the files I have to leave alone, and if there might be any others...apparently the Win 2k Registry lives under \winnt. According to the page I found, removing those files and that directory (after doing a "sys c:" from a Win 98 boot disk, to remove the Win 2k MBR) should leave no trace of Win 2k on the system. I'm thinking that removing the \windows directory from my Win 98 partition, along with everything else except the files listed above, should do the trick to remove Win 98 - but I don't want to do it until I get some kind of definitive answer to this question (I really don't want to have to reformat and reinstall....)
--AzGatekeep, Stealth Geek