I'd suggest using a fast 3.1 drive or better and install a perfect system. In your spare time. All the tools, scripts and settings you need. Minimum starting point of all the nice stuff you know you will need all the time. Then you can use resculezilla to clone it a system you want to use. Start the external drive every couple of months and make sure it is fully updated. Any new software you need that becomes your must have. (don't blow it out with random specific software as you can install it in seconds if you need it)
The UUID (I believe) would have to be changed or you could have conflicts if you boot it into a system that has a cloned system. KDE patrition manager or other managers can change the UUID # so that LInux doesn't freek out. This is a case where I can't blame it for freaking out. Seeing double.