I don't know if it was ever mentioned, but Master System manuals are slightly smaller than Genesis ones, and while the cases for Master System games look nearly identical to Genesis ones, the plastic tabs/teeth/whatever you want to call them that hold the manual in place are slightly different for Master System games.
Assuming you made these cases to be as similar to Genesis ones as possible, that means Master System manuals wont fit in them properly (they'll slide around some since they're smaller and wont stay in place).
Incidentally, Game Gear manuals are the same dimensions as Master System ones, if that helps as a point of reference for anyone.
I don't mean to poo on anyone's parade or anything, it sounds like these are really cool and could be a great boon for people needing new cases, I just wanted to toss that out there.