I would love to see pictures of the setups you used trying to track down the problems. The HAF-X employs two parts specifically for helping get air to the correct locations.
1) On the side fan, there is a shroud that can be turned to a better direction to keep your cards fed.
2) There is an internal fan + shroud that can be mounted on the motherboard side of the HDD rack that can funnel air from the front fans to the graphics cards.
A third point of consideration is that the PSU should probably be mounted with the fan on the bottom in this setup. There is a filter on the bottom for just such a setup. As it is, the PSU is taking air away from the bottom GPU.
I have tried these changes. They do make two 7990s usable (still pretty toasty though). Unfortunately, you have to buy the fan that goes into the shroud mounted off of the HDD rack and you may need to mod the shroud to get it to fit, depending on your specific cards and motherboard. However, there is no call to save an extra $10 - $30 when dropping $2000 on video cards. I recommend the higher rpm noise blockers.
@Twoboxer Yes, the FT02 should be able to keep them under control, ..., or at least keep them from having a meltdown. (Verified against a Raven RV02-e). Keeps them cooler than the HAF-X, though not by much.
Note: My tests were done in a basement where the ambient temperatures were generally 66F. To be fair, the ambient temperatures didn't stay their once these puppies got turned on. Too, bad I couldn't keep the cards as I was building for a client. Though, he did let me keep the HAF-X chassis when he decided to go with the Raven RV02-e. The GPU cooling was a little better, but I think the kicker was that he could use the exhaust at the top of the RV02-e for a hand warmer.