Your first hard drives contains the master boot record so you can't just copy some files to another drive and things just keep working. A couple of questions.
1. What hard drive does W2K reside on?
2. Why are you wanting to change your primary hard drive.
3. Are you wanting to get rid of Win98?
At this time the best thing for you to do, so as you don't lose anything would be to use a program like Drivecopy or partition
magic to move the partition to another one.
As much info as you can give us will make this an easy transition.