CONFUSION EXISTED BTWN ATC AND CARGO FLT AS TO WHICH RWY WAS GOING TO BE USED FOR TKOF AT MIA; FL.

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MIAMI GND CLRED US TO TAXI TO RWY 9L FOR TKOF. AFTER XING RWY 12; GND CTL ASKED IF WE WOULD BE ABLE TO ACCEPT RWY 12 FOR TKOF. FO REPLIED THAT DATA WAS RUN FOR EITHER RWYS 9L OR 12. GND SAID TO CONTINUE AS REPLIED BY FO. COM BROKE DOWN BECAUSE FO WAS NEW TO AN INTL FLT PLAN; PROGRAMMING A GPS AND WAS USING SOFT AND UNREADABLE RESPONSES TO GND CTL AS WELL AS READBACKS TO CAPT. GND THEN ASKED US TO SWITCH TO TWR AND TWR CLRED US FOR AN IMMEDIATE TKOF ON RWY 12. I HAD ALREADY TURNED THE CORNER FOR RWY 9L. FO SAID CLRED FOR TKOF. I LOOKED UP AND SAW A COMMUTER ACFT ON APPROX A 2 MI FINAL FOR RWY 9L. I STOPPED THE ACFT A FEW FT PAST THE HOLD SHORT LINE AND WAS WELL CLR OF RWY 9L. AT THIS TIME; TWR REALIZED THAT THERE MUST HAVE BEEN SOME CONFUSION. I BELIEVE; TO AVOID A POTENTIAL PROB TWR VERY CALMLY ASKED THE COMMUTER TO GO AROUND. TWR THEN CLRED US FOR TKOF ON RWY 9L AND NOTHING WAS MENTIONED ON FREQS ABOUT THIS. IMPROVEMENTS COULD HAVE BEEN MADE BY SLOWING DOWN AND REQUIRING FO TO BE CLR AND USE BETTER PHRASEOLOGY.