In addition to getting your foot aligned properly you might need wedges.

http://www.bikefit.com/

I started having knee pain last fall. I had ridden all summer, use Speedplay Pedals and have cycling orthotics.

I skied all winter without issues but my ski boot fitter had put a wedge in my ski binding. However, when I used my bike trainer (different bike) my knee hurt.

Saturday I had wedges put between my cleat and shoe. Yesterday, I rode for 45 min. without pain. My forefoot feels natural in the shoe. It's hitting flat across the shoe instead of pressure on the ball of my foot.

Also, keep in mind that when you make changes "less is more". To adjust to the change I'm keeping my ride time to 45 min., no hills and riding every other day.

I also have Chrondomalicia which could be contributing to the knee pain.

When we were looking at my bike we could see where the side of my foot was rubbing my crank arm. With the wedges only one spot hit so we put washers between the spindle and the crankarm to my foot away from the crankarm.