CnC Person needs Arduino code Person

I'm finding a lot of interference issues being reported about the Due with i2c, Usb, Fram, serial and pwm.
Bleed over and erratic readings.
Everything was working pretty good and after adding the Fram accuracy is gone.
I'm seeing a lot of different comments on the Fram and due
I don't think our erratic readings are from the encoder anymore.
In my reading I see default pin settings for Arduino are input high and they can cross signal each other.

I'm a bit lost now.