I think you diagnosed your problem... just keep your shoulder's parallel to the board and try not to turn your body.
I'm ducked on my twin park boards but foward stance on my free ride board. I use to have similar issues after being mostly a foward rider but you get use to it evenutally.
As to knee pain, once you stop forcing your knees to a foward stance while ducked it will get better. However, canted bindings will make it much easier on your knees, because the knees while be more naturally aligned while in a duck stance.