Read your post and happy on one hand that you have current reaching the back and that the turn, signal and hazards are functional , which means you should have no wiring issues.
Thats good, but your brake lights still don't work . Not good . Well , lets try reaching up to the brake light switch above the brake pedal and see if you can get to the switch and wires to probe them with a test light. Your looking for current going into the switch to verify if it is in fact getting current and that the fuse box is delivering . Guess you checked across the fuse and power on both sides ? That should mean switch is drawing from fuse. The switch may appear a bit complicated as it works with cruise control and other things , but you want to verify if it puts out to the line going to your rear brake lights . According to schematics I have , the 15A (fuse 9) wire is red/ lt green to stop light switch. Out of switch is w/t (white?) split into four wire splice to a LAMP OUTAGE MODULE. Out from module is LBL./w & P/W to each side & DG/W to center light.
i cannot tell from manual where this module is mounted , should be near brake pedal . As long as this schematics is correct for your model year , and color code correct , a test light will tell all as to where the current is and where it stops . If switch is putting out to this w/t wire and splices , I would look for the module and probe the preceding colored wires next. Pressing brake pedal and looking for current at the w/t wire(s) will be the first clue. Even if this diagram does not match your jeep , you will have some idea how to check system. Wiring schematics are usually accurate , but sometimes different models and options are not listed individually , hope this is right for you. My own '92 XJ will be of no help and my brother is gone for the weekend with his '2000 GC so I cannot even guess with his. Wish they still had their '98 GC . That was the ticket . :scratch: well , the culprits will most likely be the brake light switch or the module. Test light will verify what works and what dosen't.
Hope this helps , I know brake lights are important . Really, best of luck . Greg92jeepxj