Actually, I'd rather not go with a tower cooler. In building up my super cheap WMC "server" I came across some interesting research about motherboards. The motherboard I got was cheap and had a fairly high failure rate. However, someone did some resarch and found that the VRM's were failing (only a 3+1 design) on the majority of boards. That's not suprising, even if it's a 95W CPU. But the interesting part was that almost all of the failures had an aftermarket tower HSF installed. The blow-down design moved air over the VRM, keeping them cool. How much of that is an issue in a Haswell CPU with much of its VRM integrated? Not much, but it's something I'll consider from now on. And I'd rather not have to rip out everything just to put a back plate on. Yup, I'm lazy, and low on time.
That CM cooler looks promising and should fit, even with the GPU. But you're right. I'll probably mock everything up then order the HSF if I cant' find someone that's already done it. Time to get my Google on!
EDIT: Google has spoken and it won't work, not with the drive cages. I did find the Cooler Master Hyper 212 Plus does fit without issues. So, that's on my list at the moment.