Dylan–
What are you doing to strengthen your feet or to build an arch?
Your knee pain could be a running technique issue.
Have someone video tape you running so you can see exactly what you are doing.
It sounds like you have an active landing.
Make sure your heel is kissing the ground. If its not the calf is always active which is causing the problem.
Cramping is most often a hydration issue.
Have you had a PT or medical advice about the snapping tendon?
There may be exercise you can do to prevent this from happening.
Skill work to really dial in your technique so your knee is out as far as possible on every rep. This needs to be the default positioning.