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1. Yes flipping those would route them out to JX2. As long as you don't have a need for the eMMC, I dont see any issues. You will need to take into account that U1 and U2 are no longer there in your code that you used to control those mux's previously(you no longer need this)
2. Yes I believe that is still possible. I'm not sure what the Minimum MOQ is. I will reach out to you.
Also, please note, we can also do custom builds of the Rev E boards in which the JT11-JT14 are in your preferred position. These would require a minimum MOQ as well.