This will show how to edit boot.ini
You need to show hidden files for the file to show up.
Make a backup before editing.
You'll see a Windows 98 line, just remove that one.
As far as removing Windows 98 files....
Did you upgrade, do a clean install ? If you upgraded there is nothing to remove. If you did a clean install, you should have gotten a warning about another OS on the drive. Did you install to C:\windows ? If so, don't delete files, the two OS files are mixed, can't tell which ones. If you didn't format the drive you are using FAT32. I would save all the data, and re-install, wipe the partition and do NTFS.