First thing I would try is to attempt to fix the original drive so it could boot properly again. Main thing I can think of to try is the XP Quick Boot Disk from http://bootdisk.com
direct link is http://www.rloe.com/ken/xpquick.exe
and pretty much follow the instructions below for the 98SE bootdisk.
Some other ways to do it
[*]get a boot disk image from http://bootdisk.com
if the partition is Fat32 I prefer using the windows 98SE boot disk. Run the exe you downloaded with a floppy disk in the drive. Wait for it to complete. Reboot with floppy still in the drive. Many computers will try to boot the floppy first.if so welcome to DOS.
Otherwise you may need to go into the BIOS. A screen that shows up when you first boot the computer should say which key to press(will say something about "setup"). There will be instructions on the screen on how to navigate the BIOS screen. find the boot order and change it such that the floppy drive comes first. Save and Exit. Wait for the computer to reboot and with any luck you should enter DOS.
unfortunately the DOS method typically doesn't work well with usb.
[*]Get a LiveCD distribution of linux like knoppix and use it to copy the files(may require some knowledge of the unix filesystem). should work with usb or second hard drive.