Those fans do look good.

About the PSU support - I found it was strong enough to be supported by just the four screws to the case - I used the Corsair HX 1000W in my Mtn Mods cube (not an ascension). Just double check it when it's installed to make sure it's good - you can add some type of support bracket if necessary.

As for fan controllers - I'd recommend starting with something relatively simple at first - maybe the Sunbeam Rheobus, which is inexpensive and very robust. You might also check out the newer Lamptron controllers, although I've not used one so can't say. After you get it all working with the simpler controller, then you can think about going to something fancier - like the Koolance TMS-200 or the Aquaero. There are even more options for fan and temp control and display, but they can be a headache to figure out and trouble shoot, which is why I recommend going the simple route first. It never hurts to have a spare fan controller around.

The fan controllers I mentioned can easily control 3 fans on 1 channel - you'll just have to splice the fans together yourself, or use splitter cables which you can buy (difficult to make look good, but easy to use).

As for 9 fans bringing air in and 2 exhausting? It will probably work fine because the Mtn Mods cases are not air tight, but I like to balance it a bit better. Best thing to do is experiment - maybe run the fans on your rear radiator on exhaust - depends on what you are cooling as to how much difference it makes - would probably be fine for GPUs or motherboard blocks. My main concern is that if you bring all the air into the case through the rads in the bottom half, that air has to go somewhere, and it's going to want to go up. Don't know how efficient the one fan in the top half will be at drawing the air out (that's why the option for fan openings on the top panel is nice - gives you more options). Chances are, since you are water cooling everything, you're not going to have a real issue with air flow - just something to check.

One, Two, or Three loops - that's a decision you'll need to make. You easily have room for 3, but that might be more than you want. I'd probably go at least two loops, since these cases have so much room.

Also - you mentioned, I think, a concern about the bay mounts interfering with your eATX mobo tray. You can either flip your front panel - which puts your radiators on the top, or trim the bay mounts (which, I think is what you said you were looking to do - that would be my choice).

Good luck with your project!