Going with a longer spindle has already been mentioned several times. It will help you clear your heel and if you were comfortable on a triple before and are not on the compact double, it may be all that you need.
However, it sounds like you are collapsing into valgus with the right side being worse that the left and you will likely benefit from working on muscle balance around the hips. It's a lot of the same kind of motion that you worked on with your PT to correct knee alignment, you likely just need to learn to apply it to your pedal stroke and build up your muscle endurance. I'm basically talking about the same issue that OakLeaf mentioned. Foot orthotics in your cycling shoes can help correct some of the valgus collapse but ultimately, you want to address the muscle weakness that is causing it as well.
If muscle weakness leading to valgus collapse is the issue, going to a wider pedal stance may aggravate your knee pain.
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2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS