MSI Z97M Micro-ATX Gaming Motherboard with SLI Setup Issues!

Okay I see the dilemma now.

I had a similar problem with 2x Powercolor HD4850 (AMD) cards in a desktop-style case. The so-called custom coolers; heat-pipe based flower-orbs that were popular yesteryear, tended not to exhaust the heat out of the back of the cards and thus the heat never really exited the case. It just kind of stewed in it's own heated airflow, re-circulating it.
I too wedged a large fan in front of the cards like you in order to assist the heat flow from front to back of the case (a 120mm Noise Blocker - big and quiet), but it only marginally helped and again like you I felt it wasn't enough.

I think the proximity of a pair of SATA HDDs in RAID configuration near the extra fan likely compounded the problem... don't blame me it was the design of the case and where the HDD mounts were situated, which I suspected hadn't been thought through in it's entirety.

Finally I bit the bullet and made the ultimate investment to the gods of heat transfer and dissipation in the form of the now defunct Zalman Reservator 2, a black-finned aluminium tower that was not so much for overclocking but more for the quiet operation in say a livingroom-PC environment, and voila! heat removed with the GPU's running much happier!
It was a serious investment though, along with the actual Reservator (combined reservoir/radiator and pump) there was also the cost of the GPU waterblocks (x2) and Gfx-RAM waterblocks (x2), these I believe are combined nowadays, but I also included the CPU in the water-circuit CPU waterblock (with the CPU first, then the two Gfx cards in series).
I still required case-fans (for the HDDs and Motherboard; Northbridge, Power-regulators and the RAM sticks) but that is now one very quiet PC. Addmittedly I would've also liked the LED-lit fan attachment in order to "crown" the Reservator but hey, it's no longer available and I can likely build my own a little bit cheaper.

EDIT: It was my first experience with liquid cooling, and looked very nice with the clear plastic pipes escorting the blue fluid into and around the black-anodised case that matched the Reservator perfectly, a real show-piece.
Now if only I could run the piping into and under the tropical fish aquarium gravel, then all of that waste heat would become useful ;-)