Random thoughts from someone who doesn't fit into VFFs and who couldn't run in them anyway ...

Are you rolling out your calves? With mine, it often takes something narrower than a foam roller or Stick to get deep enough. Golf or lacrosse ball, opposite knee - one of the bumps of a Ma roller is what I'm using most often on my calves these days.

Most of the muscles that move the foot bones are actually in the lower legs, the deepest calf and shin muscles. The biggest difference between truly minimal shoes vs shoes with some cushion is that you'll be using your feet more. The more I strengthen my feet, the less I find that my calves are a box of rocks. But you climb, right? So your feet should be in really good shape?

Another possibility might be that the fit and/or stiffness of the VFFs actually inhibits your foot motion vs the NFs - is that a possibility?

I think some trigger points are pretty common when you do a new activity. I'd roll your calves out before as well as after.

I'm not sure I'd want to run on the road in minimal shoes even if/when my feet are strong and flexible enough for it - but there are people who do. But I think you'd want to ease into it even coming from a zero drop shoe (or short drop? not sure about the NFs).