Sounds to me that you are just over-swinging to the extreme. The force of a shoulder dominated transition to the downswing might be part of your problem. This would cause you to come over the top and certainly increase the stress on your knees.

Devote several practice sessions to working solely on balance in your swing at 60 to 70% percent of your swing speed. Most important for balance is "the feel of the body turning in response to the swinging of the club not the turning body slinging the club".

I will almost guarantee that affecting this change will improve the direction of your ball striking and make those knees feel a lot better in the bargain.