Looks like the TJ08-e is a strong possiblity. I actually had been thinking about a Desktop mini-itx form factor, but wasn't sure since that doesn't seem very popular cept for HTPCs.
The TJ08-E is a nice case, i have my gaming build running on one and about to re do it with haswell. But be warn that the frontal fan on high and low is still very noticeble, you will need to undervolt it, via software like Asus FanXpert2 (this is how i want to try on haswell) or a resistor like Zalman FanMate2 (this is how i have mine atm). The size of the Prodigy even if its mini itx is still big, its not the usual small factor case, as it does fit very big hardware that usually mini itx builds dont like big GPU or full atx PSU, full height CPU coolers, etc. With that said i think prodigy is still slightly smaller than TJ08-E, but not by much, i think the TJ08-E is a very viable option for you. Another suggestion that i would give you on the TJ08-E is get a Thermalright HR-02 Macho
, really good cooler for the money and fits very well on it, almost to the PCIe 16x, and for the gpu, i would here go ASUS GTX780-DC2OC-3GD5
, since it comes with backplate and HR02 is fairly close, this will avoid any risk if it touches (if you decide not to use the middle hdd cage as support for the gpu), beside would match the Asus Maximus IV Gene
The only bad for what you trying to do is the 2x 3.5 hdds, even though the TJ08-E can hold 5x 3.5hdds, the middle cage + 3.5 hdds will restrict you into what memory you can chose (height) and what CPU cooler you can run (or at least if you can place the CPU fan on the front of the heatsink). It would be great if you were fine with 1x 3.5 as there is a bay on bottom that can take one. On my build im going to run 1x 2.5 ssd + 1x 2.5 mechanical hdd 1tb, the real storage i maintain it on my server, personally i dont like to have a lot of mechanical hdds on my desktop builds to avoid extra noisy.
If you wish to see a lot of builds to get some rough ideas, check OCN Silverstone TJ08-E Owners Club