after re-watching the video. the seat seems low to me, because your cranks are smaller, maybe? do the smaller cranks actually alleviate the pain? i'd imagine a proper fit with proper knee alignment (think custom shoe inserts...or specialized body geometry footbeds) might fix the knee and bobbing problems all together.

hand position, arms...look great. but i definitely feel that your saddle needs to be 1-1.5mm higher---sorry to disagree with everyone else.