Try two things: a different shoe, and allow your heel to relax down so that you’re not loading the balls of your feet as you run. I find that the Lems bother my feet as well partly because of the shape. If you relax your achilles and allow the whole foot make contact with the ground as you load into the one-legged posture stance, that may help.
Other things you might look at: if you’re over striding or If you’re too upright, then that can have an effect as well because you’re pushing off and that can really load the balls your feet. So pay attention to those things and see how that goes.
Chi Running and Chi Walking Certified Master Instructor