it sound like he may be puching himself a bit soon??if he is getting severe stiffness post exercise which eases with movement he may be pushing himself a bit much into a chronic inflammation. in that case he should ease off and just try some jogging for the moment. he can also be given a program to maintain total body fitness- eg arm weights, swimming, cycling, water jogging.
from what youve said i would concentrate on deep frictions regularly (ie he may need to come in twice weekly to have any effect of these, or be taught self treatment), 5 times daily calf and hamsting lengthening, strengthening of the tibialis anterior to balance out any pull on the peroneal, possible strengthening of the gluts if these are weak. postural correction work, modification of technique(ie check his running style, see if his coach says he is doing anything wrong). then perhaps prescription insoles if you feel foot biomechanics are implicated. alot of treatment may just be slow progression back to sport. hope this helps