All that, plus try to correct your leg position from your legs, not from your feet. In Anusara Yoga, they call it "inner spiraling the thighs." Changing the rotation of the femur and knee means changing the balance of muscles in the thighs (primarily developing inner thigh muscles), which takes time, so starting with shorter rides is probably a good idea. Be conscious of your foot, knee and thigh position all the time, not just when you're on the bike. Develop your foot muscles rather than letting orthotics do all the work.

Also, the Frogs, although they have plenty of float, they'll still torque your knees when they're not on center. (DH's experience with the Frogs, not mine; but my experience with my Look cleats with 4.5 degrees of float is similar.) Float isn't a substitute for getting the toe-in right. If your shoes don't allow you to adjust the toe-in of a two-bolt cleat, you'll either need different shoes or a three-bolt cleat system.