You may want to try uninstalling the sound card drivers before you reinstall the entire OS.  It might save you some trouble.  If you decide to do a full reinstall, it shouldn't be necessary to physically uninstall the sound card.  I'd try it with the sound card in first.  If you are still having problems, then remove it physically.  If you do have to remove it physically, I suspect it is bad and should be returned.

As far as the hard drives go, you probably won't get any driver conflicts.  Hard drive drivers are pretty basic and most of it is included in BIOS itself.  You might want to unplug them before you reformat the drive Windows is on, just to make sure you don't accidently reformat the wrong drive.  I learned that one the hard way.  Safer to have them unplugged if you don't need them for the install.