Moving Windows 2003 boot+system partition

With my little experience in this domain, I can say this will nearly only depend the way your system see the disk order.

If your current PATA drive is seen as first disk by the BIOS, then once you remove it if your BIOS see the RAID as first disk, you're ok. The BIOS order is generally the same as Windows order. So if you don't have any other drive, you won't have problem.
If, later, you wan to add a PATA drive, you'll have to find a way to tell the BIOS to see it as second drive. Most BIOSes don't allow this.

Sounds like a plan, yes. But you should add a step "Make a full backup of the server" to the list.