I have a pair of utilities I use for installing older O/S versions after 2K or XP are installed. Using these two, you can put back the necessary files.
You'll need to first boot from a W98SE startup floppy and do two commands.
FDISK /MBR
SYS C:
Now you have the capbility of booting only Win98.
You next use the BOOTSECT utility (also an MS-DOS utility) to grab the W98SE boot sector from the disk, you'll need this stored in the root of C: for dual booting to function. I've attached it to this post, since it appears my link is dead right now.
You can then use BOOTPART to rebuild the 2K/XP boot manager entries and allow dual booting.
I've installed DOS several times as an alternative boot using these tools, and W98SE installation is identical, just does more after the fact.
BOOTPART - Manipulate multi-boot menu and fix 2K/XP boot files.
BOOTSECT - Read/Write MBR and save to disk