rockbiter, did you install XP on the drive that had 98 already on it?
just trying to understand your question: "did this totally wipe out my whole drive like writing zeros would?"
If you repartition a drive, unless using special tools, you will lose whatever was already on it.
When using XP , it is better to use the NT File System [NTFS] rather than File Allocation Table 32 [FAT32] system used by Windows 98.
Thruthfully a 'Clean Install' normally means starting from scratch.
Another good utility for wiping out drives is delpart.
delpart is a great little dos based ute that came with NT 3.5.
Get it at
http://www.russelltexas.com/delpart.htm
From what you have told us, i would suggest, you completely erase the drive [remove the partitions] then start your XP setup again.
When prompted, allow XP to partition the drive, then format it with NTFS.
Then let the install run it's course.
XP is pretty good at hardware recognition. But it will not find ISA cards, if your modem is an external type, leave it connected, and powered up while doing the install.
Good Luck!

Rusty.