I found a trio of 3-pin JST connectors laying around, so I labeled the "S" and "-" wires of the (stock) 2-pin X/Y/Z stop connectors, then popped the pins out and seated them into the 3-pin connectors. This will allow the stops to cleanly connect to the MKS Gen V1.4 board.
I'll need a crimp tool and some blank connectors to finish the remaining connector swaps, parts arrive Wednesday.
Separated the wires from their harness/zipties, labeled them, and noted where they'd go to on the MKS Ramps side. Some connectors won't be compatible and will require crimping, others will work as they are.