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In practice it doesn't matter whether the trace is cut or not, because the Duet normally tolerates receiving 5V into the STP pin of an endstop input. However, it is only on the 1.04 boards that we can guarantee that 5V won't damage the board.
Confirmed it was the filament. New roll works.
Got it solved. The code changes form Phaedrux helped a bunch, but the white wire dc42 recommended was ultimately the culprit.
Thanks both for your help!
now to finish calibrating it.