Rewiring Pickups (All Wiring Possibilities)
Step 1) First I remove the tape which is wrapped around the humbucker. I then remove the four screws which hold the two single coils to the humbuckers chassis.
Step 2) The wiring is now exposed. The next step is unsoldering the ground wires which are soldered to the chassis (pic 2, the red and exposed wire). I then unsolder the wire which links the two coils together (pic 2 black wires). Then I unsolder the main coils output wire from the hot wire of the 2-lead wire to which it connects (pic 2 red to clear wire). The single pickups are now independent of each other. In picture 3 of this step you can see how I plan to configure the new wiring.
Step 3) Next, I take about 10 inches of my 5-lead wire and strip one end of it, exposing the 5 wires inside. Then I fish the wire through the wiring hole in the chassis where the 2-lead wire went through. Then, I solder the exposed wire to the chassis in the same place as the wire that I removed from the chassis. Make sure to leave the other four wires with about 1 1/2 inches of length. The idea is to leave them long enough to connect to the reinstalled single coils but not so long that you have trouble taping the pickup back together.
Step 4) Now I reinstall the two single coil pickups. In this step its important to decide which wires you should solder to which. I decided to go with this: red (+) wire from dominant pickup (pickup with adjustable pole pieces) goes to red wire of 5-lead wire, black (-) wire of dominant pickup goes to black wire of 5-lead wire, red (+) wire from secondary pickup goes to white wire of 5-lead wire and finally, black(-) wire from secondary pickup goes to green wire of 5-lead wire. Before soldering the wires together I would slide a piece heat shrink tubing onto the wire, solder the two together and finally, heat shrink the tubing over the new connection to insure that there is no exposed wire.
Step 5) Lastly, I tuck all the wires in as best I can. Using the original tape which was removed in step 1, I re-tape the sides of the pickup (I used a glue stick get the tape to stick again).
Step 6) (optional) I personally like to add pin-and-socket connectors to the pickups wires for easy installation and removal without the need to whip out the soldering iron.
Check if the problem is described here, Troubleshooting Guitar Wiring.
If you still have not found the problem, I suggest you join this forum, The DIY Stomp Boxes Forum. It is an incredibly helpful resource that I have recently started to use when I need help troubleshooting. As long as you are polite and give a detailed description of the problem you are sure to get some valueable help within a matter of minutes. Most people on this forum are far more knowledgable about active electronics than I am and will be able to help you better and faster than I could.