The wire running between the distortion switch to the pot and the footswitch is an uneffected (or direct) out. Because you're moving to true bypass, you can disconnect that from the footswitch and forget about it. Although, you need to retain the white wire running from the board to the distortion switch.
I should also say that I generally don't mod pedals I can't afford to ruin, and so it would be great to hear some agreement on any of this advice from others.
I should also say that I generally don't mod pedals I can't afford to ruin, and so it would be great to hear some agreement on any of this advice from others.