Yeah I wish I could really diagnose the issues with the run game. Coming into the year I had concerns about the run game but thought at very least this team could use Zeke early and often to get in some of those body shots to wear down the defense and open up the rest of the playbook. Now granted they are yet to really stick with the run game in any situation as you said they may have the worst numbers in the league running between the Tackles. I'd have to pull the chart back up but I believe the only gap they are averaging more than 4ypc is the B gap off of Zach Martin and that is because of one rush attempt. Even if Zeke has lost a step or two he should still be able to get those consistent 3-4 yard power runs up the gut if the OL is giving him any room at all.
We really need a better well rounded back, the OL doesn't seem to be that great, McCarthy doesn't have a great history with running the ball, and you could be onto something there with Dak checking out of some of these runs too. It really is hard to say X is the problem, lets fix it. With all the presnap motion talk this year I actually think its the run game that would benefit from it. I'd love to see the Cowboys use some late motion to set up wham blocks for Zeke, use the jet motion to move the slot defender away from the play side to help open a gap off tackle, etc.