Try switching the jumper on the CD-ROM drive master\slave. Your new hard drive might have a jumper for cable select or master\slave that is interfering with the CD drive. I've had a few that required having the CD drive set to slave before it would boot.
I always thought ME was the worst OS MS released. You must have a great deal of patience. Love Win2k - I think it's the best release from MS.
Partition your drives. There's no need to have one 300GB blob.
Vmware now has a free copy. I've been running Ubuntu as a virtual machine on an XP laptop. It also has the cool feature of being able to save the state of the OS. That might be a fun way to experiment.
Cheers!