I've already created a "perfect" JJ2 for my personal use. The regular levels, the shareware levels, TSF, and HH98 all in a fairly logical order.
As for the perfect JJ1, I'm not entirely sure, but I don't think you could do much with existing utilities, like JCS94. I think it would require some extensive hacking, in which case I couldn't help you, as I know next to nothing about JJ1's internal programming. Sorry.