LTT ACFT IN CRUISE WAS GIVEN AMENDED CLRNC WHICH INCLUDED MULTIPLE LEGS. FLC HAD TO GET OUT CHARTS TO PROGRAM ACFT FOR CLRNC AS ATC ALSO GAVE DSCNT CLRNC TO DSND WITHIN THE NEXT 35 MI. FLC READ BACK AND SET NEWLY ASSIGNED ALT OF FL350; BUT AT 36400 FT; ATC INTERVENED TELLING THEM THE CLRNC WAS TO FL370.

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WHILE ENRTE TO FARMINGDALE; NY; AT FL410; WE WERE GIVEN AN AMENDED CLRNC TO FLY DIRECT TO THE PSB VOR; THEN OUTBOUND ON J-49 TO INTERCEPT J70 TO LVZ VOR; THEN AS FILED. WE WERE NAVING WITH A GLOBAL NAV SYS WITH GPS AND VOR SENSOR INPUTS AT THE TIME. THE AMENDED CLRNC REQUIRED THE PNF TO GET OUT AN ENRTE CHART TO SET UP THE NECESSARY VOR RADIALS TO COMPLY WITH THE JET AIRWAY INTERCEPT POINT WHICH WAS NOT A RECOGNIZED INTXN IN THE NAV BOX. SOON AFTER RECEIVING THE AMENDED CLRNC; ATC ISSUED A XING RESTR WHICH BOTH CREW MEMBERS UNDERSTOOD TO BE; 'DSND AS TO REACH FL350 IN THE NEXT 35 MI.' THE PNF READ BACK THE CLRNC; DIALED 35000 FT INTO THE ALT PRESELECT FOR THE AUTOPLT; AND I BEGAN DSNDING TO MEET THE XING RESTR. PASSING THROUGH APPROX 36400 FT; ATC ISSUED A R 360 DEG TURN TO RE-INTERCEPT J-49 AND INFORMED US THAT OUR XING RESTR ASSIGNED ALT HAD BEEN FL370. I STARTED AN IMMEDIATE R 360 DEG TURN; STOPPED THE DSCNT AT 35800 FT AND BEGAN A CLB BACK TO FL370. THE PNF ADVISED ATC THAT WE UNDERSTOOD OUR CLRNC HAD BEEN TO FL350; AND THAT WE WERE CLBING BACK TO FL370. ATC REPLIED WITH 'ROGER' AND NO OTHER COMMENTS WERE MADE TO US. IF THE ERROR WAS ON OUR PART; I BELIEVE THE MULTIPLE TASKS REGARDING OUR AMENDED CLRNC AND MAP RESEARCH; SHIFTING NAVAIDS FOLLOWED RAPIDLY BY A XING RESTR BASED ON DISTANCE TRAVELED RATHER THAN XING A KNOWN FIX; LED TO OUR CONFUSION. BOTH PLTS UNDERSTOOD THE ALT ASSIGNED WAS FL350; THIS MAY HAVE BEEN CONFUSED WITH THE 35 MI XING RESTR. ALTHOUGH I FEEL OUR CLRNC WAS TO FL350; RATHER THAN FL370; I'M NOT 100% CERTAIN OF IT.