The Prodigy M will fit most long cards, so nothing to worry about. Just pick any of your choice.
Mobo wise, it depends on your budget. I'd go for the Maximus Gene VII 

yes the Gainward GTX760 should be able to fit in the Prodigy-M but do be careful if you're thinking of fitting two of them as you might need to remove the 5.25" bays, single card is no problem at all

as for the motherboard, yes the Asus Maximus Gene VII is truly desireable if you have deep pockets lolz but any MATX or MITX mobo will fit, not really a recommendation but generally I'll choose one that has an x1 PCI-e lane on top of the x16 for starters.. other features are just secondary to me

oh and a modular PSU like the Silverstone Strider Plus 600W will help with the cable management as well