pronation and acl injuries

sounds neurological, but not really my area of expertise, have you tried something as simple as an off the shelf orthotic footbed or a small lift under the heel, pain in the ball of the foot is often linked to calf issues, if the muscles are compressing a nerve in the calf then it could cause such pain... most of the people i see with this type of symptom (normally not as bad) it is down to being flexed forward in a ski boot when they haven't got the available range of motion in tha calf muscle and it loads up the ball of the foot

good luck

Both feet makes a back problem relatively less likely - particularly if it's most of the feet. (Different parts of the feet are supplied by different nerve roots and it's therefore unlikely a scan will identify a discrete cause in the back itself)