ok. here are few things. First, make sure you have a win98 boot disk made. so if something goes wrong, you can always boot your system from boot disk and change the autoexec.bat/config.sys back to way it was.
the performance/compatibility messages you see are results of dos drivers loading. this actually is normal if you upgraded your window from previous version or device drivers were loaded into W98se when not needed.
here is what I would do, but remember have a backup of both files.
make backup copies of both files. both are in c:\ dir.
copy autoexec.bat autoexec.bak
copy config.sys config.bak
using explorer, edit autoexec.bat
since you are using win98se, you can comment everything out except for 'path=xxxxxxx'
open config.sys using notepad.
comment out the device for cdrom.
actually, you may want to post what's on your config.sys and autoexec.bat
this maybe easier.