This case may work for you, but im not sure how the motherboard stand offs are situated. If you search the forums you can find some like of people using aluminum boxes as cases. You might just end up causing yourself uneeded trouble with that case. Flex-atx usually stands for mini-atx, not mini-itx, you might have some size problems.
But if you really really want to do it, you can fit pretty much much anything into anything else if you really want to.
sorry, didnt see that you already bought it, post some pics of the inards and im sure that someone here can tell you what you're looking at.