I'm just thinking, why not do it the way GooFans did it? Build a website specifically for modding, and make a utility that automatically install mods. It'd be hard to make a leaderboard for Aquaria, but everything else would be doable. All that needs to be done is customize the content management software so that it's suited to mods. It's better than starting completely fresh.
(Annnnddd... I might be able to host the entire thing on my server (consisting of an Xbox), though I have no idea when I would do it, and how fast it would be if I did do it (my connection is DSL). Oh, and it's on only from 8 till 5, so I hope that won't be too much trouble.)