The JPAC has screw terminals for switches 4,5,6,7, and 8 for both player one and two (and speaker +, - and ground)
so if you cant splice into the JAMMA harness then you can do a simple remapping in MAME and use the screw terminals . For example you can screw in the wires for button 3 into screw terminal 8, then remap button 8 to 3 in mame or whatever emulator you're using.