If the ref. cooler has any strong points it's exactly that, it get's the warm air out of the case. The DCU cooler requires a case with pretty good airflow because it dumps all the hot air inside the case.
A ref. cooler wont fit the matrix card, it's PCB is very different from ref. PCB.
Running one monitor should solve your problem with it staying on 3D clocks though.
Just don't use furmark, it put's extreme load on the card. Loads you will never se in anything else then a torture-test like furmark.
You could try re-mounting the cooler on the matrix card if you think it's not properly mounted. Apply new TIM and so on, that is if the singel monitor and perhaps a few extra fan's for better airflow doesn't help.