A B747-200 WAS DISPATCHED IN NON COMPLIANCE WITH THE AUTOPLT SWITCHING UNIT REMOVED AND DEFERRED IN CONFLICT WITH THE MAINT MANUAL AND THE MEL.

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JUN/MON/03; ACFT TURNED BACK TO CARGO RAMP AFTER RPTING SMOKE IN COCKPIT. SMOKE WAS TRACED TO CAPT'S ANNUNCIATOR PANEL (ALREADY ON MEL). PANEL WAS SHIPPED TO ZZZ AND REPLACED. OLD PANEL HAD ONE ANNUNCIATOR PUSHED IN; POSSIBLY SHORTING; CAUSING THE SMOKE; ALL WIRING WAS BLACK ON THIS SWITCH. AT SHIFT TURNOVER WE WERE TOLD A NEW PANEL WAS INSTALLED BUT A GREEN; 'FD/PFD' LIGHT WAS ON. IT APPEARED THAT THE LIGHT WAS OF GREAT CONCERN. WE BEGAN THE TROUBLESHOOTING; USING THE OVERHEAD SWITCHING PANEL. WE FOUND THE 'FD/PMS' (FLT DIRECTOR/PWR MGMNT SYS) LIGHT WOULD COME ON IF CAPT OR FO FLT DIRECTORS WERE SELECTED TO A1 OR C3. ACCORDING TO THE COCKPIT OPERATING MANUAL THE LIGHT INDICATES PMS IS CTLING THE PITCH OF THE ACFT; PROVIDED THE AUTOPLT AND AUTOTHROTTLE ARE ENGAGED. WE CONTINUED TROUBLESHOOTING. WE SWAPPED ALL AUTOPLT PITCH AND ROLL COMPUTERS; NO HELP. WE FOUND AIPA SYS AND C SYS SHARED SOME COMPONENTS; CADC'S PMS SYS. WE SWAPPED CADC'S; NO HELP. REMOVING PWR FROM PMS SYS; NO HELP. WE FELT THE LIGHT REMAINING ON COULD BE A RESULT OF THE PREVIOUS PART SHORTING IN COCKPIT. WE FOUND PULLING THE PMS COUPLER RESULTED; IN THE LIGHT GOING OUT. AT THIS POINT; WE BELIEVED THE COUPLER HAD SHORTED INTERNALLY TURNING THE LIGHT ON; EVEN THOUGH PWR WAS REMOVED FROM THE SYS; AS PREVIOUSLY MENTIONED. WE TRIED TO GET A NEW PMS COUPLER; NONE STOCKED. SO WE FOUND THAT OUR MEL BOOK HAD THE BEST SOLUTION MEL 34-38A. WE CONTACTED MAINT FOR APPROVAL TO REMOVE SWITCHING UNIT AND COLLAR CIRCUIT BREAKERS. THEY APPROVED. I FAILED TO COMPLETELY READ THE MEL. HAD I REFERRED TO THE MAINT MANUAL; I WOULD HAVE SEEN PULLING THE SWITCHING UNIT IS NOT ALLOWED. BY NOT READING THE MAINT MANUAL I PUT THE AUTOPLTS IN AN UNUSABLE POS; THIS WAS UNINTENTIONAL. HAD THE MEL DDG FOR 34-38A BEEN MORE SPECIFIC AS IN 'SWITCHING UNIT/COUPLER NOT REMOVABLE' INSTEAD OF REFER TO MAINT MANUAL; MAYBE THIS WOULD NOT HAVE HAPPENED.