He wants to completely remove Windows 98!! OMFG!!
To begin with, me need to stop being a lunatic. Thenz0rz, what we'll do right, is we'll begin by altering the boot.ini like lhuser said, then stop for a pint of Carling.
Next, simply reformat the partition Windows 98 is stored on using Windows 2000. Windoze 98 uses FAT32 which is visible to the techinically superior NTFS system as used by Windows 2000, so this is easy to do just like right-click the partition on the My Computer viewing pane stop for another pint ands then just click t3h f0rm4t widget device thingy.
Then ye can do some crazy shizzle to join the two partitions together again, like one with the whole world!!!!!!11!!!!!!1!1oen
by the way, there be a utility called msconfig which grants the quaestor direct access to the boot.ini without any need for the evil witchcraft of hidden files and the command prompt.