MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
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.