MSAW ACTIVATED ON ACR FREIGHTER DURING HIS ALTDEV ALT OVERSHOT DURING IAP LOC DME APCH INTO SAN.

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I WAS RECEIVING IOE AS A CAPT IN A NEW ACFT. THE AUTOPLT WAS COUPLED FOR THE LOC 27 APCH. THE EICAS SYS ALERTED US THAT THE AUTOPLT WAS HAVING DIFFICULTY TRACKING SIGNAL FLUCTUATIONS (WE LATER LEARNED THAT THIS APCH HAS HAD FLUCTUATIONS IN THE PAST. IT COULD HAVE ALSO BEEN MOVING VEHICLES NEAR THE ANTENNA) SO I DISCONNECTED THE AUTOPLT. WE WERE WELL ABOVE SWATT INTXN AND HAD BEEN TOLD TO MAINTAIN 180 KTS AS FAR AS POSSIBLE ON THE APCH FOR TFC BEHIND US. THE PNF SET THE MDA IN THE ALT ALERT WINDOW (THIS IS STANDARD PROC ON THIS ACFT TO PREVENT AN UNWANTED ALT CAPTURE DURING THE VERT NAV MODE OF AN APCH). THIS PROC IS DIFFERENT FROM MY PAST EXPERIENCE OF SETTING THE FAF ALT UNTIL XING IT; THEN SETTING THE MDA. WE CROSSED SWATT AND WITH THE MDA SET IN THE WINDOW; I FORGOT ABOUT THE 2000 FT ALT RESTR OVER REEBO (THE FAF) AND CONTINUED MY DSCNT TOWARD 1500 FT (WHERE I PLANNED TO LEVEL OFF AND SLOW FOR THE FINAL FLAP CONFIGN. AT ABOUT 1600 FT THE TWR ISSUED A LOW ALT ALERT AND ADVISED US TO CLB IMMEDIATELY TO 2000 FT. WE WERE APPROX 2 MI OUTSIDE OF REEBO. I DID AS INSTRUCTED AND WE RPTED THE FIELD IN SIGHT AND WERE CLRED FOR A VISUAL APCH. THE MAIN CAUSE OF THIS DEV WOULD BE FATIGUE. WE WERE FINISHING THE FINAL DAY OF A LONG SEQUENCE OF TRIPS AND THIS WAS THE LAST LEG OF A 12 HR DUTY DAY. WITH THE MDA SET IN THE ALT WINDOW; AND MY REDUCED ALERTNESS; I REVERTED TO PAST HABITS AND JUST FORGOT ABOUT THE 2000 FT RESTR AHEAD OF US. I ASSUMED WE WERE CLRED TO DSND UNRESTR TO THE MDA. SECONDARY CAUSE WOULD BE MY NEWNESS TO THE ACFT AND UNFAMILIARITY WITH THE DISPLAY OF INFO. THE LEVEL OF AUTOMATION IS ALMOST TOO MUCH AT FIRST AND IT CAN DULL SITUATIONAL AWARENESS AS ONE IS LED TO BELIEVE THE ACFT KNOWS WHAT IT'S DOING. AT THE TIME; I DIDN'T REALLY FEEL THAT I WAS AT ALL INCAPACITATED WITH FATIGUE. I KNEW I WAS TIRED; BUT THOUGHT I WAS AWARE OF WHAT WAS GOING ON. LOOKING BACK ON IT; I CAN'T BELIEVE I FORGOT ABOUT THAT XING RESTR. IT WAS AS IF I WAS IN A PARTIALLY DAZED OR NUMBED STATE JUST LONG ENOUGH TO SLIP BELOW THE ALT AND LOCK ON THE MDA AS MY FINAL LIMITATION. I KNOW AS I BECOME MORE FAMILIAR WITH THE ACFT; I WILL ALSO BECOME MORE SITUATIONALLY AWARE AND WILL MORE EFFECTIVELY USE THE INFO DISPLAYED TO INSURE A SAFE AND 'AS CHARTED' APCH. FOR THE SAME REASON (FATIGUE); I THINK THE IOE INSTRUCTOR MISSED THE XING RESTR AS WELL. IT CAN REALLY SNEAK UP ON YOU. IN THE FUTURE; I WILL INCLUDE A REMINDER IN MY PREFLT BRIEFING ABOUT FATIGUE AND THE NEED TO BE ESPECIALLY DILIGENT ABOUT FOLLOWING PROCS AND PAYING STRICT ATTN TO THE ACFT'S PROGRESS ON THOSE LONG NIGHTS WHEN THE DANGER IS SO PREVALENT. SUPPLEMENTAL INFO FROM ACN 275619: WE WERE ESTABLISHED ON THE APCH; BUT HIGH. THE STUDENT SELECTED FLT LEVEL CHANGE AND WE STARTED DOWN. WE SHOULD HAVE GONE TO VNAV ON THE APCH BUT FLT LEVEL CHANGE WAS STILL SELECTED. FLT LEVEL CHANGE WAS ON ITS WAY TO 660 FT MSL; WHEREAS VNAV WOULD HAVE MADE THE XING AT 2000 FT MSL.