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My lab is researching Stage II Adult-Acquired Flatfoot Deformity, and I need a model that has the characteristic bone deformities. I was unable to find one that already has the condition. I will need to alter an existing model so that the bones are in the correct placement. However, the set of bones that I need to move are fused and labeled as the calcaneus in every model I've seen. Is there a way to alter the bones so that I can move the individual tarsals, and how wold I go about doing it so that it's not just a visual effect and alters the force distribution across the foot?

There isn't a complicated foot model built or distributed with OpenSim. You would need to build your own using the definitions used for all bodies, joints and constraints in OpenSim.

There are simple model building tutorials here and here. You could use these tutorials to figure out how to build a model programatically.

If there are lumped bones in the OpenSim/Geometry file that you want to split up, you will have to use mesh editing software to delete the unnecessary elements.