AN EMJ CREW DSNDED BELOW THE CLRNC ALT WHILE TROUBLESHOOTING A DELAYED EWR 4L LOC CAPTURE.

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STAR WAS DYLIN 2 INTO EWR AND ILS RWY 4L. HAD A GOOD IDENT FOR THE ILS; BUT FLAGS IN BOTH LOCS. QUERIED ATC ABOUT STATUS OF ILS AND WERE TOLD WE WERE FIRST TO HAVE A PROB. WHILE TROUBLESHOOTING THE PROB; AND AFTER A HECTIC LATE DSCNT ISSUED BY ATC ALONG DYLIN 2; I NOTICED WE HAD DSNDED TO 1800 FT. WE WERE ASSIGNED 2000 FT UNTIL ESTABLISHED. WE WERE CONTINUING TO DSND AND I CALLED OUT 'TWO THOUSAND; TWO THOUSAND.' THE FO WHO WAS FLYING ASKED 'TWO THOUSAND WHAT?' I REALIZED THE PROB AND TOLD HIM TO CLB AND RESET HIS ALTIMETER TO LCL ALTIMETER SETTING 29.42 FROM 29.92. WE ULTIMATELY HAD BOTTOMED OUT AT APPROX 1700 FT. ATC CALLED TO ALERT US WHILE WE WERE CORRECTING. LOC ON FO SIDE BECAME USABLE AT APPROX 12 DME AND ON CAPT'S SIDE AT APPROX 10 DME. NO IDEA WHAT CAUSED PROB WITH LOC. CORRECT FREQS AND GOOD IDENT. FAILURE TO RESET ALTIMETER AT FL180 DUE TO LATE DSCNT CLRNC WITH ASSOCIATED RADIO CALLS NOTIFYING ATC OF OUR INABILITY TO MAKE SOMTO AT 11000-12000 FT. THIS; COUPLED WITH THE LOC INOP FLAGS; ADDED TO THE DISTRS. FATIGUE ALSO A FACTOR. CAPT AND FO WERE ON ARPT STANDBY AND WERE 13 HRS INTO DUTY DAY; RUNNING 2 HRS BEHIND SCHEDULE -- HAD A MAINT PROB AFTER PUSHOUT OF RDU AND RETURNED TO GATE; AND STILL HAD ANOTHER LEG TO FLY. LOW EXPERIENCE LEVEL IN COCKPIT. CAPT'S SECOND TRIP OFF IOE LESS THAN 40 HRS IN TYPE; AND FO WITH 130 OR SO HRS IN TYPE BELIEVED WE HAD SOMEHOW DONE SOMETHING WRONG WITH RESPECT TO LOC NOT OPERABLE. ATC MADE NO FURTHER ISSUE OF ALT DIGRESSION. SUPPLEMENTAL INFO FROM ACN 650207: WE WERE MONITORING THE VNAV DURING THE DSCNT AND WE DID A DSCNT CHKLIST AT FL240. IN ADDITION TO THE AGGRESSIVE DSCNT; THERE WAS ICING. WE ADVISED THE CTLRS WE COULD NOT MAKE THEIR REQUEST AND THERE WAS NO PROB WITH THEM. ALSO; WE WERE TOLD TO CAPTURE A LOC WE WERE NOT RECEIVING -- WHEN WE LEVELED OFF.