What exactly is it that you want to do, then?
Do you want the system to boot directly into Windows?
If so, then you should simply restore the
"Master Boot Record" ("MBR") of your harddisk (i.e., the very first sector of the disk, and the place where the computer finds the instructions on how to boot from it - e.g., just drop into Windows, run GRUB, run PowerQuest BootMagic, run the OS/2 Bootloader, etc.).
If you can somehow get a Windows 98 system started (e.g., from a simple Windows 98 boot diskette), you could simply type
FDISK /mbr
That will restore the default MBR - which will simply boot into the partition that is marked
"active" whenever you boot your computer.