Board design using Cyclone V

"2.) My board functions fine appart from the above but gets very very hot. All functions and interfaces work fine, all supply rails are fine. Is this usual for a cyclone V with 300,000 LES and only 40,000 in use clocked at 50MHz? Im guessing its 40 degrees C."

40 degrees C should be still with the device's operating specs. For commercial part, if I remember it correctly, the temperature supported is 0-85C. So, 40C should not be an issue to the device's functionality.

You can double check on the power consumption on hardware vs powerplay analyzer to see if there is any anomaly on current drawn also.