AN SMA TWIN LINED UP ON THE WRONG RWY AT SJC CAUSING AN ACR MLG TO ABORT ITS TKOF AND ANOTHER ACR TO GAR.

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SJC TWR CLRED US INTO POS AND HOLD ON 30L. THE CAPT TAXIED PARTIALLY OUT ON TO THE RWY (ABOUT 2/3 OF THE ACFT ON THE RWY) AND STOPPED. HE SAID SOMETHING I DID NOT UNDERSTAND AND POINTED TO THE L. HE WAS POINTING AT AN ACFT THAT APPEARED TO BE LNDG ON OUR RWY. I LOOKED UP THROUGH MY EYEBROW WINDOW AND SAW AN SMA FLY ABOUT 100 FT OVER THE TOP OF US AND FLARE OVER THE DISPLACED THRESHOLD OF 30L. THE TWR THEN TOLD THE SMA THAT HE WAS ON 30L INSTEAD OF 29. THE SMA REPLIED THAT HE WOULD GAR; WHICH HE DID FROM THE FLARE. THE CAPT THEN FINISHED THE TURN INTO POS AND THE TWR CLRED US FOR AN IMMEDIATE TKOF. IT WAS MY LEG AND I PUSHED UP THE THROTTLES. AT ABOUT 40 KTS; THE TWR CANCELLED OUR TKOF CLRNC AND SENT THE APCHING ACFT BEHIND US AROUND. THE CAPT PULLED THE THROTTLES BACK AND PULLED UP ON THE REVERSER LEVERS. THE SPOILERS EXTENDED AUTOMATICALLY (AUTOBRAKE SYS) BUT WE WERE NOT GOING FAST ENOUGH TO ACTIVATE THE BRAKES. WE STOPPED ON THE RWY AND THE CAPT SET THE BRAKES AND ANNOUNCED TWICE ON THE PA TO REMAIN SEATED. I REVIEWED THE ABORT PROC (BRAKES WERE COOL). THE CAPT AND I DISCUSSED OUR NEXT MOVE AND DECIDED IT WOULD BE BEST TO CLR THE RWY AND VERIFY OUR PROPER CONFIGN. THE TWR ASKED US IF WE COULD TKOF FROM OUR PRESENT POS (ABOUT 400 FT DOWN THE RWY). WE REPLIED NEGATIVE. WE THEN CLRED THE RWY ON 'B;' RE-RAN THE TAXI FLOW AND CHKLIST; AND TAXIED BACK TO THE END OF 30L (ACTUALLY AT 'A'). THE CAPT MADE 2 PA'S ON THE GND EXPLAINING WHAT HAPPENED. WHILE DISCUSSING THE INCIDENT WITH THE CAPT ENRTE TO DEN; HE SAID THAT HE SAW THE SMA BEFORE TAKING THE RWY BUT HE THOUGHT IT WAS JUST A LITTLE OFF LINE TO RWY 29. IT WAS ALSO VERY HIGH. I WAS NOT UNTIL THE SMA WAS CLOSER THAT IT BECAME EVIDENT THAT IT WAS GOING TO LAND ON 30L. FORTUNATELY; THE DISPLACED THRESHOLD ON 30L MEANT THE SMA WAS QUITE HIGH AND THERE DID NOT SEEM TO BE ANY DANGER OF COLLISION AS LONG AS WE WERE NOT ON TKOF ROLL.