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Sounds to me like you have a bad brake light bulb. Those bulbs have dual filaments in them, so they can work as the taillight fine, but not light for the brake light function.
Because the 3rd brake light is working, you know that you have a signal from you stoplight switch.
You can check to make sure you are recieving signal to the socket by using a test light. Remove the brake light bulb, ground the test light clip to the chassis, and probe the brake light connector. Have someone push the brake pedal to see if you are getting a signal. If you are then you just need bulbs. If not, let me know and I can provide you with detailed wiring schematics so that you may trace down the problem.
Please let me know if there is anything else I can do to assist you.
Have you verified that you are getting signal to the wiring harness going into the connector. This will let you know if you have a wiring problem, or a problem inside the bulb connector.
You can check this by probing the brake light signal wire. See if you get a voltage signal when someone steps on the brake. You can use a test light again for this.
Please verify brake signal in the wire before the connector and let me know the outcome.
Here is the wiring diagram you requested. It will probably be a damaged signal wire because the tail lamps, stop lamps, turn signals, and license plate bulbs all share a ground together.
Here are the harness connectors so that you can find the correct wire:
Here is the ground distribution diagram:
The signal wire from your brake pedal switch goes into the bussing block under the bed. It is component #8 in this diagram. This is where you need to check for signal.