Tony,
Just to clarify...
You have two hard drives and both are formatted as FAT32 partitions? NTFS hasn't been used for the Win 2000 partition?
One can be used to boot with Win 98 and the other can be used to boot with Win 2000?
Now the obvious thing to do (if you have access to no other mass storage devices) is to dump the files from the 2000 disc to the 98 disc and reformat.
However, you say that you cannot transfer files between them because cannot access both discs simultaneously? And you say the reason is that you can't configure one or the other to be a slave?
If this is all true then - solve the concurrent access problem and getting rid of 2000 should be a trivial issue.
So in order to access both discs...
When you say the machine refuses to boot with both connected - could you get into the BIOS and see which of the HD drives could be detected? Do you have diagrams for the appropriate jumper settings (M, S, CSL)? If not I might be able to point you in the right direction if you know the drive model numbers (i.e. what type of Deskstar?)
But why does one need to be a slave at all? Do they have to share a cable? Can't they each have their own IDE channel? All motherboards have two IDE channels don't they? Can't you connect the 98 HD to IDE 1 configured as master and the 2000 disc to IDE 2 also as master?
Maybe you've got a CD drive attached to IDE 2? Or if you haven't got anything in the second IDE socket you'll probably need to get another cable.