B757 FLT CREW DSNDING BELOW PUBLISHED XING RESTR AND RECEIVES A TCASII RA WHILE ON ARR TO SFO RWYS 28.

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WE WERE DSNDING ON THE MODESTO 2 ARR INTO SFO. NORCAL SEEMED TO BE PREOCCUPIED AND SPENDING AN INORDINATE AMOUNT OF TIME GETTING AN 'ACR Y' FLT ESTABLISHED ON THE FMS BRIDGE VISUAL APCH RWY 28R INTO SFO. WE WERE ABOUT 5 MI IN TRAIL. APCHING ARCHI INTXN; WE WERE ASKED IF WE HAD THE BRIDGE/ARPT IN SIGHT. WE HAD THE BRIDGES; BUT NOT THE ARPT. WE WERE CLRED TO DSND VIA THE BRIDGE ARR. AT THAT TIME; THE CAPT WAS FLYING; DSNDING THE ACFT IN 'FLT LEVEL CHANGE' MODE TO 7000 FT. ONCE CLRED; HE SELECTED 1800 FT INTO THE MCP; AND WE BOTH 'DOUBLE POINTED' TO CONFIRM. AT THAT TIME; WE GOT A TA FROM OUR L SIDE; POSSIBLY A DEP FROM SAN JOSE. SINCE IT WAS ON THE CAPT'S SIDE; HE WAS LOOKING OUT OF THE WINDOW FOR THE TFC. AT ABOUT THE SAME TIME; NORCAL CLRED US FOR THE BRIDGE ARR LATERALLY; WHICH SEEMED LIKE AN ODD CLRNC; SINCE THEY HAD CLRED US TO DSND VIA ALREADY. I WAS THE PNF AND ACKNOWLEDGED THE CLRNC. THEN; THE TA TURNED INTO AN RA. BY THIS TIME; THE CAPT HAD A VISUAL ON THE ACFT ON OUR L AND SAID IT WAS NO FACTOR AND PASSING BEHIND US. THE TCASII WAS COMMANDING US TO CLB. WE BOTH LOOKED AT THE ALT AND IT WAS PASSING THROUGH ABOUT 5000 FT; 1 MI E OF TRDOW INTXN. THE CAPT STARTED TO CLB THE PLANE BACK TO 6000 FT. WE THEN PASSED TRDOW AT ABOUT 5700 FT. WHAT WE HAD FAILED TO REALIZE WAS THE PLANE WAS STILL IN FLT LEVEL CHANGE MODE AND NOT IN VNAV MODE; WHICH WOULD HAVE KEPT US ABOVE 6000 FT AT TRDOW INTXN. WITH THE UNFORTUNATE TIMING OF THE CLRNC FOR THE ARR; COUPLED WITH THE TA; WE FAILED TO RECOGNIZE THAT THE ACFT WAS STILL IN FLT LEVEL CHANGE MODE AND NOT IN VNAV MODE WHICH WAS THE PLANNED MODE OF DSCNT. NEITHER NORCAL NOR TWR ADVISED US OF THE TFC WHICH SEEMED TO PREOCCUPY US AT THE TIME.