TKOF ABORTED - ACR LOST PART OF THEIR NAV PRESENTATION SYS WHEN THEY HIT A BUMP AT RWY INTXN.

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NORMAL PREFLT. NO MAINT CARRYOVERS (PREVIOUS MAINT CARRYOVER AHARS 2 IN BASIC MODE REMOVED THAT DAY). NORMAL TAXI SINGLE ENG PLUS APU. 25 MIN TAXI DELAY DUE TO DEP TFC. POS AND HOLD RWY 31L (JFK) WHEN CLRED FOR TKOF; ENG RUNUP NORMAL AND STABLE CLAMP 60 KTS. APPROX 11000 FT REMAINING ON RWY 31L AFTER A BUMP OR GROOVE IN RWY AT APPROX 110 KTS. BOTH AHARS FAILED. I ELECTED TO ABORT. BOTH ENGS WORKED NORMALLY IN REVERSE AND MAX BRAKING WAS OVERRIDDEN DUE TO MORE THAN SUFFICIENT RWY REMAINING. TWR WAS NOTIFIED OF ABORT; NO EMER EQUIP REQUESTED. ALSO; A PA BY FO WAS MADE INFORMING PAX TO REMAIN SEATED. POST LNDG CHKLIST WAS COMPLETED. CAPT REQUESTED A RETURN TO GATE. BRAKE TEMP MAX 170 DEGS. NO PAX OR FLT ATTENDANT INJURIES. NOTE: MAINT REALIGNED AHARS BOTH CHKED NORMAL. CHANGE #1 AHARS. ON SUBSEQUENT TKOF FOLLOWING BUMP #2 AHARS FAILED #1 AHARS DID NOT. TKOF CONTINUED UNEVENTFUL. #2 AHARS REALIGNED IN FLT. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: THE RPTR WAS FLYING AN MD-88 ON TKOF ON RWY 31L AT JFK. THIS RWY INTERSECTS RWY 22. AT THIS INTXN THERE IS QUITE A BUMP AND WHEN THE ACFT STRUCK THIS BUMP BOTH OF THE ATTITUDE; HDG; AND REF SYS FAILED. THE CAPT REJECTED THE TKOF AND RETURNED TO THE GATE. THE REJECT OCCURRED AT 100 KTS AND THE CAPT SHUT OFF THE REJECTED TKOF SYS AND LET THE ACFT ROLLOUT TO AVOID OVERHEATING THE BRAKES. AFTER THE MAINT TECHNICIAN INSPECTED AND REALIGNED THE AHARS; THE FLC AGAIN TOOK OFF. THIS TIME ONLY THE #2; OR FO'S; FAILED; SO THEY CONTINUED THE TKOF AND USED THE ATT POS TO REALIGN THE #2 SYS THROUGHOUT THE REMAINDER OF THE FLT. THE RPTR SAID THAT THE 'BUMP PROB' HAS BEEN A CONSTANT ONE WITH THIS TYPE OF NAV PRESENTATION SYS SINCE DELIVERY.