We NEED your help!

[Dinarius]

That's an interesting problem if you don't mind such a new user chiming in. The need to organize is universal. I'd see if something like scientific name formats could help if you want to stay with numbers.
00.00.00 making room for 100 bases, 100 groups, 100 salt types or whatever the diminishing orders are. Going from -m 400 to -m 000400 or -m 30 to -m 000003 is my suggestion.