i thought about having a go at something like this myself about a year ago

to be honest i just didn't have the time/determination to get it going - hat off to you if you manage it

anyway in my research i found a bit of software you may find useful called toonboom studio - it's based on flash animation but retooled and optimised for 2D peg based animation with 3D camera movements though multiple planes - you can cut out characters from scans and give them joints on their elbows, knees, etc. and semi auto lip syncs.

think south park and you'll be in the right area (not that your characters have to look like cartman - just move like him)