Either the folder is renamed somehow (do dir \win.com /s to look for win.com in any other directory) or it's deleted somehow.
You can try if you can find a freeware or shareware undelete program that works in DOS supporting long Windows 95 style filenames, but I don't know any. But I've never looked for it either.
Unless you've got a recent backup of the whole Windows folder (and few people have so), I'm afraid the only solution will be to reinstall Windows from the Windows 98 CD or possible use the recovery CD that came with the computer.
Tried booting from safe mode
Reg. configuration error
missing or corrupted C:\windows\himem.sys
cannot find win.com
Tried booting from boot disk. Ran scandisk and the only problem was an invalid long filename that was unable to fix. Did a dir on C: there is not dir for Windows. any ideas?