I'm guessing here but drive D is a DVD drive?
DVD OS discs are all READ ONLY and can not be infected via any virus.
if 2 of the original discs ARE in fact defective then you need to take that up with Compaq for another set. further, some discs have encrypted sectors that can not be read at the dos level which is probably why you can't copy them.
most OSs have a uninstall programs feature, if this is insufficient then contact Compaq as to howto get rid of them.
the recovery partition and/or the files therein are there for your protection and modifing/deleting them is always a bad idea.
user created files are usually not targets of virus and/or hacker activity. It's always a good idea to back such files up on a regular basis, then, even if you have to install the OS from scratch it's annoying but reasonably painless.
As for making a backup copy of the install discs that may not be possible either, again, consult Compaq if such is possible, and if so, how.