Double check that you're not having disk or cable trouble, and then try to apply the builder on that drive a second time.

After that, then try the regular upgrade again. If that's still slow, then I think I updated the Drive Upgrade instructions to link Roger's information about building large drives, go back through those and see if it's helpful.

Edit: Yeah, here's what it says in the disk upgrade instructions:

Special note for large drives: You might run into a problem if your disk drive is larger than about 60 gigabytes. The builder image hasn't been updated to support large disks. It sometimes runs out of memory when building the music partition. This will manifest itself as disk drive errors when the player boots or when you try to put music onto the player. If this happens, there are two things you can try: You can try to apply the builder image a second time (starting the procedure from the top). Sometimes this is enough. You can also format the hard disk manually.