I think that you more than likely need to take a day and spend some quality time with your computer cooling, testing as many different cooling configurations as you can dream up, even those which would sound like they make no sense. During the entire process, and using a pen and paper, make a diagram of your case and number each fan location (ie lower front intake = F1, upper front intake =F2, Rear Exhaust = R1, Front Top Exhaust = T1, and so forth). Then, start with just 1 intake, and on your chart, record the temps at say the 5min mark of Furmark or P95 or ideally something that stresses everything equally, for the CPU Package, Each Core, GPU1, GPU2, and any other temp sensors you have (ie MB, PCH, etc). Use HWMonitor since it gives you all the temps and you will rule out the variable of using multiple programs. Be sure that fan configuration is written down as well.
As you go along, add one more fan back each time. Then, start flipping fans and recording temp changes. Try going from side intake to exhaust, top intake vs exhaust, etc. The only fans not to bother flipping are your front intake, although you could try a reverse airflow where you intake behind the case and exhaust through the front fans.
This is what will determine the best airflow configuration for you. There are many people who think that more fans always equals better cooling, but it doesn't (except for with radiators or heatsinks, ie push-pull is always better, but how much better is the question) . What makes for better cooling is having smooth, unobstructed airflow with a clear path through the case, which is able to contact all necessary components, and then leave, and do this all as absolutely fast as possible. The longer air is in your case, the lower it's cooling ability and it will in fact begin to insulate, rather than conduct, heat. When you start adding fans "just because" or are essentially trying to spot cool everything, the airflow pattern becomes nonexistent and instead you have a bunch of little vortices of air blowing around but not moving anywhere.
I would suggest that before you do this, take out all the components, clean out the case with soap and water, clean the components with a strong air compressor and IPA if needed, and disassemble the fans, clean the blades with a damp rag and IPA followed by a few drops of multipurpose or "all in one" lubricant (I personally use Group IV or V synthetic motor oil, specifically Redline 0W30 or Royal Purple 5W40; Redline, a Grp5, is an ester based true synthetic and has immense cleaning powers compared to other oils as well as an extremely high resistance to shearing; Royal Purple is a Grp5, meaning PAO, true synthetic and is also an excellent cleaner while providing enormous resistance to mechanical wear). I recommend the two mentioned Syn Oils because I have been using them for all my fans since '04-05, and I have not had a single bearing failure, even with cheap Thermaltake Sleeve-Bearing 80mm and 92mm fans that ran 24/7/365 for 7 years, and which run perfectly to this day, even with a number of them having been used horizontally (aka the quickest way to kill sleeve bearings)! It also quiets fan motors, and results in more consistent speeds according to the fans' own tach read outs!
When you reassemble everything, take TIM and make sure that the entire case is as bare of cables as possible. Now, I realize that some showing is inevitable, but the ones that must be visible, route them along preexisting "obstructions" that, unlike the wires, can't be moved (ie case pieces, behind the motherboard, along the back bottom/side corners of the case, etc). Don't stuff your HDD cages full of wires, as most intakes blow through the cages.
In fact, remove any unused drive cages, or if you can't remove the cages, at least remove any unused drive sleds. Position the drives you do have as evenly spaced with as much distance between them as possible, or depending on the layout you may want them all in the lowest or highest possible bays, all crammed together.
Remove the PCI slot covers for all of the unused expansion slots. As a positive pressure setup is ideal, this will give the GPU heated air as direct and easy an exit as possible.
Cut out the integrated fan grill in the rear Exhaust fan mount, and watch the airflow double while the noise decreases dramatically.
I personally think that with air cooled multiple GPU setups, there is one thing that is vital: have a second set of fans that mirror the front intake fans but mounted on the inner side of the drive cages, creating a push pull effect to greatly increase the effective static pressure of these fans, and to ensure your GPU's are being provided with as much cool air as quickly and directly as possible.
That's about it for now, but I am confident that the above would show you a significant difference in not only temperature but also noise.