Originally posted by apokalipse
if you transfer an OS you will not be able to use it as is, you will need to either "repair install" or reinstall the OS to "adapt to its new home"
Although this is true for the Win 9x OS as well as ME, This isn't always the case with Win2k and almost never the case with XP (registration aside). Although there is some work involded in getting drivers and old junk removed, the OS has enough sence to know what is needed and install what it takes to work. That is only if you are using the standard IDE interface, as the OS has a set path to the HDD location, so it might not find it on SATA, SCSI or an expansion card.
I have had issues in the past with the Linux Boot loader causing hickups. There is a utility that can be used to remove it (the name eludes me), but then you also need to clear the partition of the Linux File System. As I don't think windows can even address it.
The drives would be spec'd as c, d, e... for however many partitions you create. Partitions are seen as new drives, unless you mount them as a folder in an existing partition (NTFS). This isn't really all that bad, but if the drive fails, it's all the same and everything goes... Just to keep it in perspective.
You may just want to install win2k over the win98 install and leave the rest. But that is up to you to decide. Win2k will work fine on FAT32 and all of your files will be intact. The 10gb Linux partition if you delete it, could be made into a useable partition for win2k and then you will have your C (50gb) for the OS and the D (10GB) for whatever.