As your glutes and hamstrings fatigue toward the end of a run, your ankle pronates more due to inward hip rotation which would overstress your posterior tibialis tendon which goes behind your medial ankle to the inside of your arch. The hamstring fatigue lengthens your slowing stride which makes things worse.
As your stride lengthens and you slow, you heel strike more and your foot tends to slap sown. In order to prevent toes from slapping you employ the toe extensors and anterior tibialis eccentrically. The toe extensors pass through synovial lined tendon sheaths for lubrication. The synovial sheaths can become inflamed and even swell.
If you run faster, you land flatter, so you should try speeding up about 10%. When you fatigue, you should walk until you can run fast with good form. When you are too tired to do that, you should just walk.
Running with poor form just trains poor form and fatigues you for the next training session, lengthening recovery time.
Running down hill causes more stress on the anterior tibialis and toe extensors as they try to slow your forefoot down at the increased angle. The answer is to lean slightly forward on your ankles and shorten your stride which will have your legs moving faster but less ankle angle.
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