it may be the footbed. Not that footbed is bad for you, but it may more that you are wearing them too long. With any custom footneds/orthotics you have slowly introduce them to your feet. Like you wear them 2 hrs first week and add 1hr each week etc. Pay attention to how your feet are feeling.
Your body probably is in proper alignment now so you may be using muscles you havent used before (may be why your knee hurts).
New boots, new foot beds and full day of riding, you are asking for trouble.
Wear the foot beds everyday in you walking shoes. (wear them couple hours per day and slowly increase the time you wear then)
From my experience, your feet gets tired and sore when you first use foot beds, but not any kind of pain.
So take it easy first week or two.
I don't think that this is the issue. I've had orthotics in my shoes for the past 4 years. I don't have foot pain while just walking around, but they just feel "better". These are just newer ones.
I might just go back to the factory footbeds and see how those are....