>> Now I understand better what you want (though still stay on my own :)

Yes, I think I'm beginning to understand what I wanted to ask as well. It's hard to state the exact question when one starts from a point of not knowing anything :)

I think the approach I will take is to write an emacs command in Perl (I only use Lisp once in a blue moon). The command will go through the functions in the buffer, and then reconcile those with the descriptions in the METHODS section beyond __END__. It'll allow one to re-run the command to add function descriptions (for functions you've left off), without altering what you've done (it'll do a diff of sorts), as well as flag functions you've deleted (which won't work perfectly for changing the names, but...). So by following some simple conventions I'll be able to keep the method documentation separate from the code (I'll probably put a line or two at the head of each function, but then extended docs below __END__).

This will let me have code that is both maintainable and more readable than the mix in way.