I don't remember exactly, but i think there is a limitation on the size partition windows 98 will make. You may want to try to reinstall XP.
As for getting rid of unwanted partitions, linux has a powerful tool called dd that will solve that. bear in mind this is if you want to destroy all data and near the beginning of the drive (mbr, partition table, everything).
dd of=/dev/hda if=/dev/zero bs=1M count=20
I don't remember how much space the beginning of the drive requires, the above example kills the first 20 MB (way overkill, I know). With the partition table wiped clean, there will be no residual linux to give you troubles.
of = drive you want to overwrite (not partition, the drive itself)
if = what to overwrite it with.
bs = block size
count = number of blocks
You can use a linux boot diskette as was recommended, or a bootable CD (such as knoppix, from www.knoppix.org
) to get at it. You need to be root, I believe.
Good luck, I hope you haven't given up on linux. It is nice to have a windows installation around to start with though.