you should keep those application's install packages and all system drivers stored separately and ready to run so that is not a hassle when they need to be deployed.I consider that a last resort. It took eight days to configure Windows just the way I want it (installing programs, drivers, etc.) A HUGE hassle.
keeping those along with backups of user files & application data(settings, etc) make this whole process very simple each time it needs to be done.
what seems like a HUGE hassle is what your going through now.