As you'll get better quack using the bridge side of your bucker when split, I'd switch positions of your neck and middle pickups if they are the same wind. That way you get N up on your middle pup (you did that mag test on the string side of the pickups and not the control cavity side right?).
Then there are two options for polarity. If your singles are like most, they are wired so the "hot" wire is out of electrical phase with the humbucker (note we have to worry about two "phases". What you want is magnetically out of phase but electrically in phase).
Given your current setup is S up middle and black hot is causing an out of phase issue, put your single coil hot wires back to stock and use red hot, black and white together, green ground. If you want the better sounding bridge coil plus middle in pos 2, switch your neck and middle, do white hot, green and red together, black ground.
