Eidolon's Inn covers some very basic assembly, which I already know.

The hardware docs are somewhat useful but a bit sparse. It also doesn't look like they've updated in ages...
I contacted cdoty last night and got a response this morning. He's the only one I know that's developed a game for the MegaCD using the neodev package. Unfortunately, he didn't give a lot of information either, and his site says you need to actually purchase his game to get the sourcecode so that's out for now (while $19.99 is certainly not very much to pay for a game, the idea of paying that much for access to sourcecode is a lil crazy imo...).
So I guess I'm back to square two (yeah, square two...cdoty's site at least explained the hellish process for putting together an image so I don't have to go all the way back to square one at least).