I think the NoiseBlocker m12-s2 is a great fan, but i would go with S1, i own 7 on my server, and they spinned around 850 (not 750 like the specs says in mulitple mobos) not sure if all are like that or were just a batch, atm my TJ08-E has noiseblocker pwm (not the M12 but the standard) between 800-900rpm and fairly quiet, over that it starts to get noisy, so S2 is like 1250rpm... i think the S1 is a better choice. The fan on the Mugen (slipstream pwm 300-1600rpm) depending on the mobo/software it can be droped around 300rpm where its inaudible, even toward the 600 is still ultraquiet, past 800rpm it start to get noticeble under a quiet enviorement, over that i can hear it always. So thinking on trying to aim not to go over that, i think the S1 is a better match, or another Scythe Slip Stream 120mm x 25mm PWM Mid Speed Fan - (SY1225SL12LM-P)
could be an option, as it will match the CPU fan, and since its pwm it could be controlled the same way as the cpu fan (depending on the mobo).
As i said in my case the HR02 almost touches the GPU, i had to use the hdd cage for sustaining the GTX580 and at the same time my GPU is thiking due to the card comes with a backplate, so for me wasnt about touching and shorting... but more not to stress the cpu socket. The Mugen 3 is smaller but not by much in width so it will be close, the GTX660ti is a smaller card, so might not reach the hdd cage for support, not saying it will touch with the gravity on the card, check OCN Silverstone TJ08-E Owners Club thread
, it has multiple builds there that might help you get a better idea.
Also check OCN [OFFICIAL] ROG Maximus V Owners Club
(not pure on the micro atx version but has some), i saw a build there with Coolermaster212 + 7870 (direct CUII) + PS07 (same case for practical purposoes), and seems to fit fine, i expect similar with mugen 3.
While the frontal fan is not quiet, imo is a good fan in terms of cooling, even at low rpm moves a ton of air (a big strength of TJ08-E is its cooling), so i would test this first, specially undervolted around 500-600rpm is pretty decent. The phobya is suppose to be quieter, i read some when i was deciding what to do, but also narrower and don't have the penetrator style so it wont push as much. As i said i think its better just to install a fanmate2, set the fan to low rpms and this should drop it between 500-600rpm, play with the fanmate for your desired cooling/noise. If you feel it still is too noisy you can swap the fan.
Personally i think its best to invest on a better mobo than the fan mate, like the Asus Maximus V Gene Motherboard
, its $60 more (not sure on your side, but you will also save on not needing the fanmate and buying the phobya), it suppose to allow undervolting pwm and 3pin fans, so it should allow dynamically undervolting on the frontal and the back fan, the only thing that im not sure is how low it will allow on the none cpu sockets, as in my case GENE IV it has a cap of 60% on none cpu fans, but a lot of people reported that with FanXpert (software provided by asus to control the fan via mobo) they were able to, some said couldnt, depended on the version, but this is with version 1, now FanXpert2 seems much better, still i havent played with it so i can say for sure, but this is what im betting for a refresh when Haswell is released, and if Gene VI is released. Here is a video for you to check the how it is the FanXpert2, Cool Tech: ASUS Fan Xpert 2 Demo - Take Control of Your Fans
and ASUS Fan Xpert 2 Tutorial and Overview
Edit: adding pics n links