Windows boot problem

I have a desktop pc running on windows xp sp3 with two internal disk drives C & D
Windows was pre loaded on to drive C: which also has files on it. Drive D; just initially had files on it
Last year I had a boot problem and ended up buying a new copy of windows xp and loading that on to drive D: as I could not repair the windows on drive c:
Now the same problem has happened and the only way I been able to correct it is to partition drive D: and load a fresh installation of XP on to that partition.

The computer is now working, but I am left with, Drive C: corrupted boot but files are still accessible.
Drive D: with a corrupted boot and files on it. and drive D: partition with a working copy of windows and a few files.

How can I get back to just one drive having windows loaded and still be able to access all the data.

I have AVG, Avast and Comodo loaded and have scanned for viruses and deleted a few that showed up.
This has still not repaired the damaged boot sectors.

I would also like to have drive C: just for windows and all the other files on drive D: That way if windows does go down again I could just reformat and reload windows without loosing any files.
If I do boot from C: how do I then make D: the working drive ?

The system has a raid set up; promise 1+0 stripe/raido scsi disk device. But I know nothing about raid setups.

I previously had to replace on of the drives so C: drive is original 80gb D: drive is a replacement drive 500gb

Any help would be much appreciated.
John