Stacie, how old is your son? I am a middle school teacher and he sure sounds like he might be an early adolescent. I know you said your school was bad (believe me, I have worked at some of those schools), but what kind of communicatipn have you had with them? Any feedback as to what is going on with his behavior at school, besides the low test grade? Although I might say if you are really frustrated, let the "natural consequences" take effect; failing grades, not passing classes, maybe having to retake a class, not get to do sports, or other negative things (no video games?). It sounds like he needs an organizational coach, to work on time management, using his planner, setting daily and weekly goals. You can certainly do this, but you sound really frustrated. Perhaps you could work with the school psych. or counselor. Or, there are people who do this for a living. It usually costs a bit, but a month of coaching might help you set up a program.
You should schedule a meeting with his counselor and/or team. Our first step in this situation would be to have teachers in each subject sign the daily planner and make sure all of his needed materials are in his backpack at the end of the day. Then the parent checks the planner each night, initials it and writes any comments for the teachers about issues with homework or long term projects. We also do weekly emails regarding progress. Are your school's assignments on Schoolnotes.com? It's a very commonly used web site where teachers post their work for the week. That way, you are aware in advance of what is coming up.
As far as the run goes, what are you training for? I know I never could have done any event with my kids at that age. My son who is now the super athlete, in the Marines, complained bitterly when I would ask or make him come with me to hike or x country ski, etc. He discovered the joys of cycling on his own after I stopped trying to get him involved with other things.