James – have you checked out the “The Big Muff Page” here: NYC Muff v9
There’s also the Kitrae Big Muff site: NYC Classic Muff v9
Should be able to suss out the wiring from the info supplied in the photos from those two sites . . . .

If not, perhaps a better photo of the existing stompswitch wiring and where they go could help us better help you. As it is, we can only guess at which jack is “In” and which is “Out”. Normally, the input jack has the battery grounding switch. But it’s always good to verify. Do you know if it’s the “Classic” or the “Reissue”?