*sigh* I knew -z had you PM me before I even read this thread. I've only modded three cases and looking forward to the 4th. HW should be considered for his hands on concerning WCing. I'd investigate what he offers. Zepper has reviewed many cases and his postings are not to be discounted. Zap has...I sign my PMs to Zap, GrassHopper

He has built and helped more ppl with gaming boxes than he would care to count. I'm sure.
He posted in this thread and I agree with him re. front to rear air flow.
I bought a full sheet of modder's mesh, 36"x42" and half is left. It was used for fan grills and intake air grills. Both Lian Li cases had the front panel cut open, 5.25"x7.25", modder's mesh bonded inplace, then home a/c filter material used to clean the air.
Given the above. When your selected case first came out, it was like WOAH a filter! But it was short lived. Bad mouthing someones case selection is like laughing at thier shoes. I won't do it.
Given your PSU/case selection, this is what I would consider.
Use the side window case. Use just the lower of the two 120 exhaust fans. Block the upper 120 fan port for the time being. Mod the window for a 120 that will blow on the PCI slots but still cover the graphics cards, a tad below the graphics cards. Cross-Fire will offer up some for real waste heat
The mesh side cover will offer dust in and noise out. The side panel fan could be filtered. This is just my opinion because many love thier meshed Lian Li and Stacker cases.
With the windowed case in stock trim, this is what I see happening. The user needs more air because SLI/Cross-Fire is to dang hot. So he adds uber-flow 120s all around. The filter stiffels the intake and the twin exhaust end up stalling air flow through the PSU. jonnyGURU has seen PSUs in a back flow condition from strong case negative pressure..YIKES!!
Ppl forget to count the PSU as an exhaust fan. The PSU's fan is the second most important fan inside the case. CPU fan is first. Graphics will just shut down when hot. Generally.
The S12 has a silent fan and won't win a fight against two 120 exhaust fans. Your Raptor is known to run very warm and side-saddel mounted HDDs don't get the best of air flow. It's not bad mind you, it would be better with the cage turned 90 degrees.
ATM, my next case will be the Akasa Eclipe 62 @ $146. I don't want an insulated case and this case offers 2-120 fan ports plus a slide-out tray. The intake would be modded as the LLs were. A little more noise but much better clean air flow.
...Galvanized