knee: stop iaido, very tough on knee, unless you doing the standing kata. also, in aikido, pay attention on how you do tenkan, you might be torquing the knee, smaller footwork, i.e. shorter stance; of course, some aikido style preferred longer stance whereas for me I preferred to do aikido like I am taking a stroll in the park.
shoulder: human body works in balance, front balances back, left balances right. tight back, stretch front. tight left, stretch right. tight ass, knock head.