I am running the same case and motherboard, I couldn't be happier. I managed to squeeze in a Noctua D14 rather than run water on this rig though.
Before you get a PSU, make sure it fits! As others said, it is SOOOO tight getting a PSU into the Prodigy.
As for watercooling, I would recommend a x355 pump instead of the D5. They are quite powerful and have a footprint that is easier to manage in a SFF water build.
Also have a look at the performance-pcs.com liquid cooled Prodigy -- it's one of the cleaner builds I've seen that includes both top and front mount rads:
Performance-PCs.com, ... sleeve it and they will come
G'luck.