CASE: what would you suggest as a cool enclosure near the price range of the CM 352?
You should point out where you will buy those parts, so that we can be aware of relevant prices.
Just as an example: you say that the Big Shuriken 2 costs less than a Kotetsu. In Italy (where I live), Germany (where I often buy) and U.S.A. (where I sometimes buy) usually it isn't so, as there's often a slight price premium of the Big Shuriken 2 over the Kotetsu. So, to try to advice you, we should know your current prices.
Anyway, at first glance I would look either to a Fractal Design Core 3000 or to a Bitfenix Prodigy-M.
For some money less, perhaps you may look at the Antec One, Corsair 230T and NZXT Source 210.
For some more money, you may take into account the Fractal Design Arc R2 Mini.
All the quoted enclosures, except perhaps the Fractals, surely deserve a fan swap, as well as the Silencio.
SSD: mx100 SSDs shuld work up to 70°C, so it should be ok
An high running temp will heat up your enclosure, and it's not advisable, noise-wise and reliability-wise. Look for temps and go for the M500 whether they were significantly cooler.
PSU: Silverstone SST-ST30SF and Corsair CS are in the same price range of the Seasonic G-360, slightly cheaper than the E9. Which would you choose?
For a Core i3 I would pick the Silverstone unit, for a Core i5 probably the Bequiet E9.
Now... the S-version dilemma: i5 4460 and 4440s are the same price. I guess the power consumption and noise are similar when idle. Any reason to pick the S-version over the standard one? Should I spare 50€ and go for an i3 4330?
There's no compelling reason to pick a S-SKU, unless they cost less, IMO.
With the right motherboard you can always achieve similar thermals with any regular SKU, just adding a small negative vcore offset inside the BIOS, while retaining a bit more speed (yes, I'm talking about undervolting a regular CPU).
The Core i3 may be preferable (money-wise) whether your coding/video-editing apps don't use more than two cores (as often HT just sucks).
Whether you should go for a big tower CPU heatsink, you might take into consideration a low end videocard along with a Pentium G3258 (the so-called Anniversary Edition).