garrett
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yes, the drawing from J.E.L. is very similar to that. and yes, I have 4 conductor P/U's. the hot or red lead goes to the Volume pot, the Braid to ground, and the green and white leads are pigtailed and no connected to any component. The volume works like a volume, I just have to remember not to go past 9 when rolling up. the tones work more like distortion, adding more or less as I roll that dial up and down.
this is the assembly card provided with the harness:
Correct, but the two pots on the right in your pic are meant to be the volume controls. Pickup should go to the open outside lug. Out to switch goes to center lug, shared with the cap.
Note how the tone controls in the diagrams have the center lug to ground. Nothing should connect to those pots except the cap and grounds.
What you have in reality doesn't match the diagrams. Unless you really like it wrong* as is, you'll need to disconnect your pickups and output wires, rotate the harness 180 degrees, and rewire to the diagram.
*Non standard is more accurate. You may really like it as is, but just know that it is not vintage nor modern style wiring. You have created an alternate scheme and that works differently.