If you have copies of all your important data, then yes, you could remove the second hard drive, and then install Windows again on the first hard drive by following these steps to be sure your new Windows installation is free of infections:
You should run Killdisk to delete everything including any infections. This is a free progam and can be downloaded HERE
. Put the program on a floppy disk or a CD.
Then run a DOS disk, such as a Windows 98 start up disk, when the computer boots to DOS, type "C:" (without the quotes), push ENTER. Then type "fdisk" (without the quotes), push ENTER, then just push ENTER at each selection that you are prompted to make (in other words, just accept all defaults). You can download what you need HERE
Then reboot with your XP CD in the cd drive and reinstall Windows, being sure to choose "Full Format" instead of quick format when prompted.
Be careful about reinstalling your data as it may contain a virus or other malware.
Just make sure you have everything you need before you start. Create the Killdisk disk. Create the DOS disk. Make sure you have the XP Disk and Product Key. Make sure you have the motherboard drivers (if needed). Etc.
If you have any other questions, just ask. We will be happy to guide you through this process.