ACR LGT ALT DEVIATION OVERSHOT DURING CLIMB FROM AUS. FO HAD SET AN 'OFF' TO PREVENT NUISANCE ALERTS ON APCH AND FAILED TO RESET PRIOR TO DEP.

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JUST AFTER TKOF FROM AUS; RADIO CONTACT WITH DEP CTL COULD NOT BE ESTABLISHED DUE TO THE CAPT'S BOOM MIC TX. THE F/O HAD TO MAKE INITIAL CONTACT AFTER CLBING TO 5000'; WHICH WAS THE ALT PUT INTO THE ALT ALERTER. THE CLRED ALT WAS 4000'. THE ACFT WE WERE FLYING WAS AN LGT AND IT WAS VERY DIFFERENT FROM THE REST OF THE FLEET. ALTHOUGH THE NONSTANDARD C/P HAD NOTHING TO DO WITH THE LACK OF XMITTING CAPABILITY; IT WAS JUST ONE MORE PROB. THE ACFT HAD MANY DISCREPANCIES. THE LEFT SEAT HAD NOT MADE A TX EXCEPT ON THE INTERCOM TO THE GND CREW; SO THIS PROB HAD NOT YET BEEN DISCOVERED. OTHERWISE; THE ERROR IN THE 'CLRED TO' ALT WOULD HAVE BEEN DISCOVERED IN TIME TO LEVEL OFF AT 4000'. THE F/O EXPLAINED WHY SHE SET IN THE INCORRECT ALT. IT WAS HER HABIT TO GUESS AT THE CLRNC INITIAL ALT BEFORE LNDG--SHE NO LONGER DOES THIS. SHE WAS RUSHED AS THE CLRNC WAS NOT READY UNTIL WE WERE 'PUSHING' AND SHE SIMPLY FORGOT TO SET THE CORRECT ALT INTO THE ALERTER. SUPPLEMENTAL INFO FROM ACN 92129: ON APCH AT AUSTIN; TO AVOID NUISANCE ALERTS; THE F/O HAD SET THE ALT ALERTER TO 5000'. THE ALT ALERTER SOUNDED AS THE ACFT CLBED THROUGH 4000'; APCHING THE 5000' SETTING. AT THIS POINT; THE FLT CREW WAS UNAWARE THAT THE F/O HAD NEGLECTED TO RESET THE ALT ALERTER WHEN THE CLRNC WAS RECEIVED.