A D328 CREW; UNABLE TO COMPLY WITH EWR TWR'S REQUEST OF S-TURNS ON FINAL; EXECUTED A GAR. WHILE DOING SO; THE CREW OVERSHOT THEIR ASSIGNED ALT.

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INSIDE OF 2 MI FROM THE AIRFIELD; THE TWR CTLR ASKED FOR AN S-TURN SO THAT HE COULD GET A DEP OUT. THERE WAS A GREAT DEAL OF CONFUSION ABOUT THE RWY AS THEY WERE NOT OPERATING IN NORMAL CONFIGN DUE TO THE CLOSURE OF RWY 22L AND THEY WERE JUST OPENING THAT RWY AS WE WERE ON APCH. THE CTLR THEN ASKED FOR ANOTHER 'BIG S-TURN WHEN WE WERE AT 1000 FT AND VERY CLOSE IN TO THE RWY BECAUSE HE HAD TFC LNDG ON RWY 29. THE CTLR THEN ASKED IF WE COULD USE RWY 29. THE APCH AT THIS TIME DID NOT MEET STABILIZED APCH CRITERIA SO WE INITIATED A GAR. I INITIATED THE MISSED APCH; MADE THE CALLOUTS TO WHICH THE FO DID NOT RESPOND. HE DID NOT PUT THE ALT CLRNC IN THE BOX WHICH CAUSED ME TO FLY 400 FT ABOVE THE CLRED ALT WHEN I REALIZED WE HAD BEEN GIVEN 2000 FT. I ASKED FOR THE CORRECT ALT IN THE BOX SEVERAL TIMES BEFORE HE RESPONDED. MEANWHILE THE FO DID NOT RESPOND TO MY CALLOUTS FOR FLAP CONFIGNS. AS I WAS TRYING TO LEVEL AT THE ALT HE NOTICED THAT THE FLAPS WERE POSITIONED AT 12 DEGS. HE RETRACTED THE FLAPS WHICH CAUSED THE ACFT TO SINK 300+ FT BECAUSE I WAS ALSO UNDERGOING A PWR CHANGE TO CTL THE AIRSPD AND ALT. THE CTLR WAS REQUESTING THAT WE RESPOND TO THE ALT CLRNC. I ALSO NOTICED AT ABOUT THE SAME TIME WE WERE GOING 240 KTS WITH THE FLAPS OUT. ALSO A FLAP OVERSPD CAS APPEARED.