As a long time user of Minox and Minolta cameras, I don’t understand why you believe that Minox negatives would deteriorate any faster than 35mm. Therefore I don’t see the point in your elaborate project.
As for printing, besides the Minox enlarger, there are Minox negative carriers for most populous enlargers such as Leica, Beseler, etc. Or go hybrid and scan negatives to computer.
Filing and keeping track of those little negatives can be a pain. However, storage and filing is important. The best method is the one devised by Minox and now made by third parties into which negatives are inserted and can be examined without touching.
I assume you have all of the Minox accessories, such as Minox viewer, etc., which can make life easier.
I am currently on the road, but if you visit the Minox heading at photo.net you can find vender for Minox file envelopes.