hmmm....you may
read this article and try to see if something works for you....
Btw...do you have "ordinary" win98 or win98se? As you will read...there are 2 registry checker tools (scanreg.exe and scanregw.exe) try running both of them....and if not...reboot into command prompt (hold F8 key at boot and select Command prompt from the menu that shows up...then try typing/running scanreg.exe and/or scanregw.exe)...
Also...have you tried manually searching for those "missing files"? Are they there or not?
Ok....read that article above...and try those procedures...then let me know if problems still exist...hopefully not...
Good luck!
p.s.
You should consider upgrading to some WinXP alike OS....because as far as i know there isnt much support (if any!?) anymore for Win98...so your system if far more vulnerable to both....such system errors....and also to hackers (although up-to-date antivirus/firewall/spyware/adware solutions may help you alot here). So my advice is to upgrade asap!