First, get the appropriate wiring schematic from Van?s Aircraft. It will save you countless hours and frustration.
Second, those autopilot disconnect button extra long wires with pins on them were designed to be run up to the WH-RV12-Optional (25 pin connector), pins 9 and 12. I would suggest you go into the avionics bay and disconnect the WH-RV12 Optional from the WH-00026. Then check to make sure you have matching pins. If not, then you need to run those AP button long wires from the disconnect button to WH-RV12-Optional. That is probably clear as mud; but a little time studying the wiring schematic should help clear it up.
In the plans, you may want to reference pages 44A-05 and 42C-08. While all those instructions are great during the build, you get a better overall picture with the wiring schematic.
Have I said ?wiring schematic? enough times?