Has she got any positive neurodynamic signs upon testing? (Slump, Passive SLR - ??possible Sural nerve bias) Symptoms sound a bit peripheral neurogenic in nature, especially the latent and prolonged onset of symptoms after activity. Her nerves may be a bit more sensitive with the correction of her longstanding faulty lower limb biomechanics by the way of her orthotics, which may also have an affect on the mechanics of her lower limb nerves, triggering some neural signs and symptoms upon higher impact activity like running?

She may need to gradually increase the time spent wearing her orthotics before attempting higher impact activities like running. Lower limb neurodynamic assessment and treatment may be a consideration?

She may also need to address other factors including training intensity, running technique, reinforcement of correct warm up / stretches / cool down after running etc.