RWY INCURSION BY A BE36 BONANZA PLT AFTER HAVING SOME DIFFICULTY WITH THE PERCEPTION OF THE TWR CTLR AT MRY; CA.

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I WAS CLRED TO LAND RWY 28R AT MRY. I ADVISED THE TWR THAT I WAS PARKING AT FBO X. HE ROGERED ME AND STILL CLRED ME FOR RWY 28R; WHICH WAS ON THE N SIDE OF THE ARPT. AFTER LNDG; THE TWR CTLR ASKED ME MY INTENTIONS. AGAIN; I ADVISED HIM THAT I WAS PARKING AT FBO X. HE ROGERED ME AGAIN AND TOLD ME TO TAXI R AND CONTACT GND. I TAXIED CLR RWY 28R AND WAS TAXIING ON THE PARALLEL TO THE W JUST PAST THE TAXI EXIT AND THE TWR CAME BACK WITH 'ACFT X; SAY INTENTIONS.' I RESPONDED AGAIN AND TOLD HIM THAT I WAS ON THE PARALLEL INCHING DOWN AND GOING TO GND FOR PARKING AT FBO X. HE THEN TOLD ME TO REMAIN ON HIS FREQ; TAXI TXWY B AS REQUESTED. TXWY B INTXN WAS DIRECTLY AHEAD OF ME NOW SO I TAXIED JUST OVER THE HOLD SHORT RWY 28L LINES WHEN I CALLED TWR BACK AND REQUESTED THAT HE CONFIRM THAT I AM CLRED ACROSS RWY 28L. AT THAT TIME ANOTHER CTLR; PROBABLY HIS SUPVR; IMMEDIATELY RESPONDED; 'NEGATIVE; HOLD SHORT.' I DID WITH HALF THE ACFT OVER THE HOLD SHORT LINES. THEN THE SAME CTLR SAID TO TAXI ACROSS RWY 28R. I DID AND ASKED IF HE WANTED ME TO STAY ON HIS FREQ OR SWITCH TO GND. HE SAID STAY WITH HIM AND TAXI TO FBO X. THERE WAS CONFUSION ABOUT WHETHER THE PREVIOUS CTLR'S CLRNC INCLUDED XING THE ACTIVE RWY. I FELT THAT IT DID; BUT CHKED ANYWAY. I WAS THEN CONFUSED TO WHETHER I WAS TAXIING AS THEY REQUESTED. I'M STILL NOT SURE.