You will have to stay under 80mm for the cooler(the above Noctua will work with the bottom fan in place.). Honestly having the power supply help remove heat may not be a bad idea. If you can find a very slim fan like the Scythe Slipstream Slim it would fit on top of that cooler in the case(but just fit).
It may be a good idea to have the fan push air into the power supply to get rid of the heat because the case has no other good way to remove heat.
Another thing you will have to consider is using low profile memory and make sure the board does not have the cpu socket too close to the pci-e slot if you plan to use it.