I've helped others in another forum who have easily installed and booted Windows from any primary partition, not just the first one.
In fact, it is even possible to boot Windows from a logical partition with a little bit of work. But if you move Windows from one primary partition to another one, in the least you will have to change the C:\boot.ini file so that it specifies the correct Windows partition; that may be all you need to do. Your boot.ini file should look similar to:
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows XP" /fastdetect /NoExecute=OptIn
So "partition(2)" would mean windows is on hda2/sda2, but only if sda1 is not labeled as an extended partition; Windows only counts primary partitions and logical partitions, not the extended partition "container". Let me know if your boot.ini file is correct, and we can work from there if you want.