I've been wanting to do that myself, seeing as I have all the taped episodes from both MTV's and The-N's runs of the show. Unfortunately, they aren't perfect; some of the commercial bumpers from the MTV broadcasts faded to black quickly, and there were audio dropouts on a couple of episodes. Add to that the fact that the Season 5 end credits were replaced by MTV advertising and other garbage, rather than the standard credits/alter-egos, making things even more challenging.
That's where the The-N broadcasts come in, of course. Much of their audio can be spliced in to make up the difference. Naturally, there are problems here, too, not the least of which is their editing of episodes (read: brainless censoring), and skipping entire episodes altogether, in order to shield sensitive minds (think of the children!) from "objectionable" material that their Degrassi broadcasts were already indulging in! (God, don't get me started on this topic...)
The good news is that I'd already done virtually all of this work when I captured the episodes and converted them to DVD-R years ago, so I know what kind of challenge to expect. The bad news is that I lost the raw source files in a hard drive crash; the project files that I have left aren't really in an editable condition, meaning that I'd have to re-capture the audio all over again.
A more immediate project might be to preserve the original broadcast of "Is It College Yet?", as the versions on DVD are the edited-for-time ones (MTV claims they lost the source tracks for the full version, without which they could not replace the original music), as well as other Daria-related special material (such as Behind the Scenes: Daria, hosted by Janeane Garofalo, and Look Back In Annoyance, the D/J-hosted retrospective that aired the night before the IICY premiere).