Is overheating of either/both of the two fpga's the only thing that can cause throttling?  Or are there other factors that can cause a single to throttle?  I removed the heat pipe, the old paste was uniformily spread on both chips, cleaned up the old and reapplied some new stuff making sure it too was uniformily spread.  So far the highest I can go is with the 808 firmware and that might throttle a handful of times an hour.  Temperatures consistantly reported between 44-46C.  Any firmware above with throttle every 3-4 minutes.  The only thing that I forgot to check for was that both chips are sitting in the same plane, but by looking at the even distribution of the thermal paste, I would guess they are.

Also, as an FYI in case the front led stops working for any one else (or falls out like mine), the two leds on the right side will go out for about 12 seconds if the unit throttles.  Although, I did go out on a limb and was able to reattach the led that fell off.