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Nice make. Flipping the cooling fan works with your modification, but I don't see why it's necessary. Your observation that the zero position changes is correct, and that is pointed out in the description. This was designed for a v3 Mega (dual z-endstop with heated bed) with a v6 clone hotend and trigorilla titan extruder clone. I don't have a Mega-S to fit test it on, but if you have specific changes, please share so I can improve.