I've installed the MakeMkv application, and it is quite nice. Very quick conversion and the CPU temps stay fairly low. Didn't go much higher than the 117F you quoted.
Handbrake takes much longer and thrashes the CPU.
I recall that you raised the INTAKE and EXHAUST fanspeeds on your 8-core Mac Pro in order to lower the Northbridge temp. Did you not pursue this on your 4-core movie server mac pro?