AFTER CHANGING FROM THE PLANNED RWY 29 DEP TO A RWY 11 AT EWR TO ACCOMMODATE ATC'S REQUEST A CPR GULFSTREAM CREW FAILS TO RESET THE MAINTAIN ALT REQUIRED FOR THE RWY 11 DEP RESULTING IN AN ALT OVERSHOOT.

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WE (THE CREW) RECEIVED OUR FULL RTE CLRNC FROM NEWARK CLRNC DELIVERY. AS PART OF OUR CLRNC TO IAH; WE WERE ISSUED THE NEWARK 7 INST DEP. AS WE AWAITED OUR SVCS TO BE COMPLETED ON THE GA RAMP; WE PROGRAMMED OUR FMS'S WITH OUR FULL RTE CLRNC. BECAUSE THE WIND WAS OUT OF 350 DEGS AT 8 KTS; AND BECAUSE WE WERE GEOGRAPHICALLY CLOSER TO RWY 11/29; WE INITIALLY ANTICIPATED; BRIEFED AND PROGRAMMED RWY 29 INTO OUR NAV COMPUTERS. PRIOR TO TAXI; WE CONTACTED EWR GND AND THE CTLR ASKED IF WE COULD ACCEPT RWY 11. WE ELECTED TO ACCOMMODATE HIS REQUEST AND RE-BRIEFED OUR DEP FROM RWY 11. I; AS THE PNF; FAILED TO RESET THE ALT SELECTOR FROM 5000 FT INITIAL ALT OFF RWY 29 TO 2500 FT INITIAL ALT OFF RWY 11. WE DEPARTED RWY 11 AND WERE QUICKLY HANDED OFF TO NY DEP CTL. WHEN I INITIALLY CHKED IN WITH NY; I VERBALLY SAID WE WERE OUT OF 2500 FT FOR 5000 FT. THE CTLRS IMMEDIATELY SAID 'OH REALLY; YOU SHOULD BE LEVEL AT 2500 FT COMING OFF RWY 4.' I IMMEDIATELY ANSWERED THAT WE INDEED TOOK OFF FROM RWY 11 NOT RWY 4; TO WHICH HE SAID THAT THE INITIAL ALT SHOULD HAVE STILL BEEN 2500 FT. THE CTLR DID SAY THAT TWR SHOULD HAVE ISSUED YOU THE INITIAL ALT ON OUR TKOF CLRNC (WHICH THEY DID NOT). BY THIS TIME; WE HAD ARRESTED OUR CLB AT ABOUT 3800 FT MSL. I IMMEDIATELY QUESTIONED THE CTLR ABOUT RETURNING TO 2500 FT IMMEDIATELY! HE SAID TO MAINTAIN OUR CURRENT ALT AND DO NOT CLB ANY HIGHER. SHORTLY THEREAFTER; HE ISSUED US A FURTHER CLB ALT. BEFORE LEAVING THE CTLR'S FREQ; I APOLOGIZED FOR OUR ERROR AND HE SAID THAT IT WAS OK AND NOT TO WORRY ABOUT IT. TO THE BEST OF OUR KNOWLEDGE; THERE WERE NO AIR TFC CONFLICTS DUE TO OUR ERROR. SUPPLEMENTAL INFO FROM ACN 597201: THIS WAS THE 4TH LEG OF AN 8 HR FLT SCHEDULE DAY.