Don't change the heatsink configuration unless you absolutely have to. Turn on a front fan. It'll be fine. If enough air is moving through the system, it won't be in contact with the heatsinks long enough to warm up much.
A nice logical setup with airflow from front to back is good. Don't mess with it. If you have any heat issues (which I doubt) then just add a few more intake fans to the case. In tests, additional intakes (known as a positive pressure configuration) works better than extra exhaust.
Also: You do not need heatsinked memory. You only need heatsinks on memory for looks and/or if they're going to be over-volted. Since you're not going to overclock the system, just buy memory that will fit under your CPU heatsinks, with fast base clock numbers. IE DDR3-1333 (Aka PC3-10600) or higher. Don't worry about timing stats,
Intel chips like fast memory speed (AMD chips prefer fast cycle timings) for maximum speed.
Your software is the issue here Dave. It's not using your GPU correctly with either current AMD or Nvidia cards. I think they may be buying into the bandwagon of requiring professional grade cards for video rendering (Nvidia's Quadro and AMD's FirePro). Nvidia for certain has cut the processing power of their consumer cards in half for the past few years, which will definitely have an impact on render performance.
I don't have any kind of sensible solution here, the only way to get more render performance involves going to a pro grade card, and one that will match or exceed your current consumer card will cost thousands.
Other thoughts: Supermicro make awesome dual CPU boards. Every dual chip board I've ever used (from Pentium 2 days onwards) has always been Supermicro, and they've been rock solid reliable.