Nick:
At the 2009 Summit, there was a lot of interest in organizing the rules by general subject/topic. I don't remember exactly who took it on (I think it was Mike B), but version 1 of 2009 rules and each issue since have been organized by broad subject. That said, I don't see any possible way to maintain existing rule numbers and retain said organization OTHER (don't even bother DCJ001) than to have section or group identifiers and then rule numbers under each section/group starting with Section A, Rule 1, Section A, Rule 2, Section B, Rule 1, Section B, Rule 2, etc.
Unless the above or something similar is done, there just isn't any way that I can think of to maintain some semblance of structure. Even then if a rule is combined with another or just dropped entirely, the rule numbers that follow in that section will have to change the next time (assuming a new rule is not promulgated to replace it).
If you can come up with an alternative, I am sure the BOD will be more than happy to consider it.
Chet