Now that the design is pretty close to being finalized at this state, I will be searching for manufacturers to produce the first prototype. If you have any suggestions or things to look out for please let me know.
Another thing worth mentioning which I haven't thought about until now is that you can actually install a 3.5" hard drive if you are using a direct plug dc-atx psu such as the g-unique.
Protocase is fucking crazy. I'd talk to local fabricators if I were you for prototypes. Usually cheaper that way then you can make the adjustments needed and go from there. You could always try talking to sliger too.