Getting to the MK bus drop off early morning is a problem. First, World Drive (the road that goes to the MK bus loop & Contemporary) is one lane only. They take turns letting cars go in each direction, but that can take a while. Second, the course sometimes goes across the bus loop entrance. The course varies slightly in this area, but some years the runners go in the employee entrance just past the bus loop, which means that buses can't enter the bus loop until the runners are all past that area. Until that area is clear of runners I believe all the buses will drop off at TTC so people can Monorail/ferry over. That said, they usually try to clear the MK of runners before the park opens. The first runners start at 5:30, with I believe the last runners starting about 6:15-6:30. As they need to maintain a 16min mile, and mile 5 is just before the park, and mile 6 is just after the park (approx), even the last runner to start, taking the full 16min allotment, they should be at mile 6 by 8:05-8:10 (6:30 + 6x16). So if you have PPO dining, or just like to be there really early, it may take longer and you may go via TTC. But by the time the park is open, MK transit should be back to normal.
The other parks shouldn't be impacted, some routes may take longer than normal due to road closures, but the WDW bus drivers should be well aware, so just allow for a few extra minutes when trying to get to places.