Hey everyone, just following up. I did end up removing most of the rocks and redirecting the waterfall with foam. This did fix the problem, for a few days until I was actually able to observe the actual problem. What was happening is that the waterfall pump's output would drop,causing the top waterfall basin to drain, filling the pond up above the drain in the skimmer box. Eventually, the pump would pick back up, putting out the correct amount water, but having lost water down the drain, the pump would begin to starve.
I have since removed the pump, hoping to find it plugged or dirty. Unfortunately, the bearings are seizing up in the pump. I am currently in the process of rebuilding it, an Aquascape SFA4500, with new seals, o-rings, and bearings. I currently have it apart and will be picking up the new bearings and seals this Friday. I know there are a number of people on here and other forums looking for how to rebuild these pumps, so I will be putting together a tutorial with pictures and part numbers/sizes.
Thank you all for the advice so far. I currently upgraded the fountain pump from the 350 to a 550GPH to at least keep the pond clean until I am able to finish fixing the waterfall pump.