I can only speak about the National Kidney Foundation 5K I did at Epcot in March 2008. Here is the route:
Start in parking lot and run east, then north, then back towards the park.
Enter the backstage area where the external part of TestTrack is.
Turn right and run around the back of Wonders of Life, entering park through cast member entrance near where the wand base used to be.
Run down middle of park and walkway to WS.
Run around WS from Mexico to Canada.
Run back to front of park, exit through gates, and finish back in the parking lot.