Unfortunately there currently are no 990FX-based motherboards that are made for mITX cases like the Bitfenix Prodigy. At least that I'm aware of. You will need the i5-4670K for that.
At the moment, I don't think so. Closest I found was this board, which *claims* to be mini-itx: http://www.dhgate.com/p-ff8080813dd1653f013dea080a873fef.html
However, looking at the picture, I'm fairly sure it's really micro atx form factor - there are two expansion slots and if it weren't for the northbridge, there would be room for a third without interfering with the rear ports. Also, there are six mounting holes, while mini-itx boards only have four.