I watched a bunch of the Towson game (so you don't have to) and first off HOLY POOP I WILL NOT MISS FLO.

Second off, the runs seemed to work finally, with a different approach. Clearly interior runs are going to be a problem, and part of why the passing has been such a success is that teams have been selling out to stop the run. A bunch of the TDs came as Towson had both safeties up on the line, so if you beat your one man, you're home free. So, it's possible for a defense take away one element of your game, and I think some teams have just been doing that for the JMU zone runs.

Ways to combat that are:
1) bite the bullet and throw it. CoJo has the head and the arm for it, and with a little play action, there will be a lot of open men. There are plenty of ways to stretch the field both vertically and horizontally, and throwing deep at will and whining about "we can't run it like we used to" is like getting a free Porsche and complaining about the paint color.
2) misdirection runs. Some of the plays that really worked against Towson were faking inside zones and then running the other direction, sweeps, and other things. Sure, we all prefer just run it right over guys, but if they won't let us, then just use other tools.

This is a pretty good offense, and a truly superior defense. As long as we don't give up dumb penalties or waste plays on no-gain runs that we have proven we can't do, we should have a deep run.