Windows not booting

I have a strange and complex situation-

I have a PC with Windows XP and 2 hard drives. Windows stopped booting
on the C drive. So I took out that drive and put in a spare drive and
installed windows on it so it would boot. I can now access the second
drive, retrieve the files from it, and then put in the original C
drive as the second drive. Then I hope to either grab the files from
it as well and scrap the whole thing, or, better yet, work on it to
get that OS to boot.

This leads me to several questions 1) Can I set the HD (jumpers?) so
that when I turn the PC on I have a choice of OS to boot from, so that
if I try something to fix it, I can test it without taking the whole
thing apart each time. How would I do this?

2) I don't know how to work on the OS when it's on a secondary
drive...when I open the Control Panel for instance from the start
menu, it will be the CP for the main drive...correct? I'm not sure if
what I'm asking even makes sense, but it seems like I would have to
find the controls and settings and tweaks for this drive in the system
folders instead of thru other Windows means (start menu, Run command,
My Computer, etc)

3) Third, I'm not sure how I can fix the OS anyway - it was working
fine, the last thing I was doing was finding tons of spy/mal/ware on
the drive, using adaware to delete them, and that's where it got
stuck. A while before that I also used some instuctions to turn off
the logon/welcome screen, setting a admin password and set to auto
login. I had not yet rebooted after this, I wanted to delete the
spyware first. It got so stuck that I had to pull the plug. After that
it would not boot, even in safe mode. It would just scroll thru a list
of files and then stop. I also tried to do a windows repair, where it
would ask for he admin password, and then just drop me to a prompt
C:/Windows and just sit there. So I'm not sure what I can do to fix
this or how I can acces what I need to access to fix it since it will
now be a secondary hard drive.

Thank god for these news groups....thank you all for the many past and
I'm sure future posts that I have recieved so many good answers from.