A B747-200F ON TKOF CLB AT 4000 FT HAD #1 ENG PYLON AIR DRIVEN HYD PUMP ACCESS DOOR PANEL DEPART THE ACFT.

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PRIOR TO DEP IN ZZZ; MAINT WAS WORKING ON THE #1 HYD AIR DRIVEN PUMP AND HAD OPENED THE PYLON 'BAT WING' AND ENG COWL DOORS. BOTH WERE CHKED PRIOR TO DEP. WE WERE DISPATCHED WITH A 'DZUS' FASTENER INOP AND IT WAS IN THE LIDS FOR THE #1 PYLON BAT WING DOOR. AFTER TKOF WITH THE GEAR AND FLAPS RETRACTED; CLBING THROUGH 4000 FT WITH AN AIRSPD OF 250 KTS; A VIBRATION OCCURRED FOR APPROX 5-10 SECONDS. VIBRATION WAS EQUIVALENT TO A NOSEWHEEL SPINNING DOWN AFTER GEAR RETRACTION OR A GEAR DOOR REMAINING OPEN. THE VIBRATION SUDDENLY STOPPED AND THE ACFT AND ALL ITS SYS WERE OPERATING NORMALLY. AFTER LEVELOFF; WE TURNED OFF THE AUTOPLT TO CHK THE ACFT TRIM. THE TRIM WAS NORMAL. AT THE FIRST WAYPOINT PAST TOP OF CLB; WE NOTICED THAT THE FUEL BURN WAS HIGHER THAN IT SHOULD BE AT THAT POINT. ALL FUEL GAUGES WERE TESTED AND NO FAULTS WERE OBSERVED IN THE SYS. WE WERE IN COM RADIO RANGE FOR COMS WITH DISPATCH WITH OUR POS RPTS AS WE BOTH CONTINUED TO MONITOR OUR FUEL STATUS THROUGHOUT THE FLT. THE FIRST 4 HRS OF THE TRIP WERE AT NIGHT. THE FO WENT TO THE MAIN DECK TO CHK THE FREIGHTER'S VIEWING PORTS; BUT IT WAS DARK OUTSIDE AND HE COULD NOT SEE ANYTHING. EACH SEGMENT OF THE FLT EVEN THOUGH WE WERE AT THE CORRECT ALT FOR OUR WT; WE WERE SLIGHTLY OVERBURNING COMPARED TO OUR FLT PLAN. AFTER SUNRISE; THE SO WENT DOWN TO THE MAIN DECK TO LOOK OUT THE VIEWING PORTS TO INSPECT THE ACFT. HIS RETURN TO THE COCKPIT INCLUDED A RPT OF THE #1 ENG 'BAT WING' DOOR ON THE PYLON WAS MISSING. THROUGHOUT THE REST OF THE FLT WE 'THE CREW' AND XYZ DISPATCH MONITORED OUR FUEL BURN AND WE FIGURED OUT THAT WITH THE CURRENT OVERBURN OF FUEL WE ESTIMATED OUR FUEL ON ARR IN XYZ TO BE 24000 LBS; WHICH IS NORMAL. WX IN XYZ WAS FANTASTIC AND DISPATCH COMMUNICATED WITH JAPAN ATC TO INSURE NO DELAYS ON ARR. WE LANDED UNEVENTFULLY IN XYZ WITH 26000 LBS OF FUEL USING ONLY THE #2 AND #3 REVERSERS NOT TO COMPOUND THE DAMAGE TO THE #1 ENG AREA. AFTER PARKING THE ACFT; THE CREW INSPECTED THE PYLON AND DISCOVERED A SMALL HOLE IN THE #1 FUEL TANK ON FAR OUTBOARD INSPECTION PANEL.