There will always be locked system files, even if you don't have any applications running.
If it will boot or not depends on what you do. A formatted primary partition set as active will be bootable.
Next time you can try: extract the iso to a small primary partition. Make the partition active. Use bootsect /nt60 to create a correct boot sector (if xp has formatted the drive). Put the harddrive back and install Windows.
Linux is one of the exceptions. Without shared gfx, you should be able to use all of it as normal system ram. The pae kernel is not restricted as in Windows.
I think I see where we misunderstand each other. You are talking about maintaining the data on the drive while creating the array. I'm past that (the OS can be ghosted to another 3rd drive) :)
Why do you think that? From the OS's perspective there is no difference in addressing the data. The OS is not concerned about the physical layout (LBA numbering is the same before and after).
A reinstall shouldn't be necessary. You just need to make sure Windows has access to the raid driver. It is a bit like switching from pata to sata. You can google a how-to guide.