Your D Drive on most manufactured PCs is going to be a read-only partition that is designed to hold only your recovery files. These are files that would be used to reinstall Windows in the case that you booted to the "recovery partition" and not the recovery disc.
Now the C Drive is what holds all of your data.. if you use the disc and perform a recovery, all of your data will be lost!
If you are completely sure that your D drive is a separate hard drive, or separate partition that you created, then it would not be affected by recovering Windows on the C: partition.
While the D: drive may have been the "host" for some infectious files in a case like this, Windows was stored on the C: drive. Therefore, all of the startup programs, services, and drivers were being loaded from the C: Drive. In theory, the C: drive held everything that triggered the files from the D: drive to open up, if there was a virus being held there.
Therefore, upon recovery (assuming the D: drive is a partition you made) you could perform a full virus scan on the D: partition. Use a few different programs (Kaspersky, Trend Micro, McAfee, Spyware Doctor, ect.) to get a ranged analysis of the drive. Once deemed clean, you should be able to trust the files on the drive and use them as you always did..
(To clarify, the files will not open by themselves like they are right now. Upon restoring, unless you begin to open files on your D: drive without scanning them, they pose no threat whatsoever).
I will say if you used the D: drive as your data partition only for music, ect.. the likelihood of an infectious file being there isn't too likely. The source of the virus (perhaps an infected EXE you downloaded) may be there, but the actual infectious .DLL files for example that were being run at startup, are usually stored on the C: drive.
