AN ACR FLC FLYING A B747-200 FROM JFK FAILS TO VERIFY THEIR PDC WITH TWR RESULTING IN A TRACK DEV AND TFC CONFLICT.

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I WAS CAPT OF RESCHEDULED B747 FLT FROM JFK TO EHAM (AMSTERDAM). WE PICKED UP CLRNC VIA ACARS WHICH READ 'MERIT 2 DEP PUT TRANSITION RWY HDG TO 1.5 DME THEN TR HDG 100 DEGS.' THE ATIS SPECIFIED DEPS ON RWY 31L. THIS CLRNC IS UNUSUAL FOR RWY 31L DUE TO PROX OF LGA ARPT. HOWEVER THE MERIT 2 DEP SPECIFIES RADAR VECTORS IF NO SPECIFIC CODED CLB IS ASSIGNED. SINCE THIS WAS OUR SIT IT MADE SENSE. IT WAS JUST UNUSUAL NOT TO TURN L OFF RWY 31L. I MADE A NOTE TO VERIFY OUR CLRNC WITH THE TWR. WE WERE ASSIGNED RWY 31L FOR TAXI. WE WERE CLRED FOR TKOF WITH NO FURTHER INSTRUCTIONS. HANDED OFF TO DEP; I RPTED CLBING TO 5000 FT AND IN THE R TURN TO 100 DEGS. THE REPLY WAS 'ROGER; CLB TO 7000 FT.' AFTER A FEW SECONDS WE WERE TOLD TO TIGHTEN THE TURN AND MAINTAIN 3000 FT; THEN TIGHTEN THE TURN HDG 130 DEGS MAINTAIN 2000 FT. WE SAW TFC FOR LGA OFF OUR L AT ABOUT 1 MI. ATC ASKED WHAT OUR DEP CLRNC WAS. WHEN WE TOLD HIM; HE SAID THE TWR HAD ORIGINALLY CLRED US TO RWY 4L; AND THAT THOSE INSTRUCTIONS WERE FOR THAT RWY; AND WHEN THEY GAVE US RWY 31L THEY EXPECTED US TO FLY ONE OF THE SPECIFIC L-HAND PROFILES; EVEN THOUGH WE WERE NEVER TOLD WHICH ONE. FIRST OF ALL; WE NEVER HAD ANY MENTION OF RWY 4L WHATSOEVER. ALSO; WE FOUND OUT THROUGH OUR COMPANY PEOPLE THAT OUR CLRNC WAS ISSUED 2 HRS EARLIER WHEN RWY 4L WAS IN USE; AND THEN IT WAS NEVER UPDATED FOR US. I'M UPSET THAT THIS OVERSIGHT WAS MADE BY JFK. I'M UPSET AT THE RIDICULOUS EXPLANATION THEY GAVE US; AND OF COURSE I'M UPSET WITH MYSELF FOR NOT SECOND-GUESSING AN UNUSUAL CLRNC.