Make sure that you ice those sore parts as you get them. This is something my trainer makes me do and it always helps. About 20 min is all you need a night until it isn't sore anymore. The knee thing sounds almost like an IT Band being a bit tight. If it persists you may want to foam roll that sucker. It hurts like hell to do it but that is the only way I know to make the IT band be good.
Nice workouts btw and I see your cals are up a bit. Do you feel better now?
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