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planks & side planks - held each for 90 seconds or so...my shoulders were super tired and they gave out before my hips did 
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Yeah, it frys the shoulders. It should sort itself out pretty quickly though as it's mostly and endurance thing. Ninety seconds for the side planks already is pretty good. Get the regular planks up to at least 2 minutes...when your shoulders can take it
. It ain't a walk in the park.
You should find as the glutes and posterior chain in general gets stronger you will have less problems with the knees. Also ankle mobility can play a part as well as hip mobility. From time to time though the knees can get achey when you do a lot of squatting and a little switch like this can fix them up but basically it's the all squatting and little else that leads to this. Squatting is good for the knees in some ways but they will not in themselves cure a weak a relatively weak PC. Just the opposite, really, a strong PC can help cure a bad squat.