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Alright thanks a lot for your inputs, I'll go figure out how to work with this. I guess I could hold the MCU in reset mode to make sure all IOs are in Hi-Z state, right? Would that too have any adverse effect?
Thanks for the idea of sharing the layout, this seems really interesting. Since I get 5 boards, I could use two and put up a pair, one with the on-board peripherals unconnected.