After reinstalling the heatsink with a torque screw driver I can report back that everything is running cooler now.
Temperature difference between CPU A and B between 1 and 7 degrees (1 at startup, 5 at light usage and 7 under full load). Temp difference between CPU and heatsink 15 degrees under heavy load. Both heatsinks warm up. Without fan rules modification i get low 70 degrees C under full load (handbrake) on CPU A and if I increase both CPU fans to 2400 it cools down.
Machine is still amazingly quiet.
Under light usage both CPUs are between 40 and 50 degrees C and I think I do not need to modify the fan speed. That means I have the same level of sound emitted as with my 2x 2,4 GhZ setting.
Under heavy load I increase the rpm of the fans slightly (CPUs > 2300 and the rest >1000-1100) in order to have a lower temp, but the machine is running still at almost the same sound level when stressed out.
So anyone who is interested in putting two X5690 in their MAC PRO: yes you can, and yes it will still be the same quite machine you bought.
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I would like to thank h9826790, lexR and JronMasteR as well as all the others for their support!