Are you familiar with Frankenstein or Pet Cemetery? You're asking about raising the dead here - even if it is only a Quark document.
My experiences with MarkTools have been mostly bad. Documents I've salvaged using it are not exactly the way I saved them and often have hidden little problems. One file had a tiny little empty text box on the pasteboard of a Master Page that had been divided into 999 columns. It took me forever to figure out why it wasn't printing. On top of that, the XTension that installs with the software ended up corrupting otherwise perfect files as I saved them - precisely what the software was designed to prevent (if I can find the email I got from Markzware tech support, I'll post it. Essentially it could be summed up by saying "Oh well, sucks to be you")
I think you would be better off investigating why your jobs are corrupting rather than delving into the black arts in an attempt to bring them back from the dead.