OK, some questions and suggestions:
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Can both hall effect boards be the same size? If we can make them identical you only need one board instead of two and most board houses give you between 2 and 10 identical boards on a single order. One board saves money and reduces the work a bit.
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on the board with 50 (instead of 49) sensors, where is the non working (or at least not needed) sensor? It may be easiest to put in all 50 sensors on both boards (if there is room) then just not put a sensor at the non working position. Does that non working position change the pin numbers to the mega at some point or is it just skipped?
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Do you need mounting holes on the sensor board? If so where and what diameter are the mounting hole or holes.? They are simple to add to the board if I know where they are.
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When I started at making the wiring in schematic I noticed the sensors are on the pcb backwards (i.e. the pins are 1 2 3 rather than the correct 3 2 1). I assume that is important because the sensor is probably only sensitive on on one side. I am correcting that now and will post in a corrected sketch in a bit.
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The connectors on the mega: it is possible to get Dupont connectors and a crimping tool on Ebay. That gives you a plastic housing that takes the 6, 8 or 10 wires on the mega and a wire coming out of it for the connection. It is then possible to make a clamp that will hold the connector in place (because you have a longer strip of plastic to work with). That’s probably what I would suggest doing. That may be better than soldering wires as if something breaks you can unplug it rather than having to unsolder wires.
Peter