ACR LGT CONTINUED LNDG ROLL ONTO STOPWAY INSTEAD OF EXITING THE RWY AT THE END AS CLRED.

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BOSTON WX WAS VFR AND THE TWR WAS IN THE PROCESS OF CHANGING RWYS AND CHANGING CTLRS. ON SHORT FINAL TO RWY 27 BOSTON TWR REQUESTED THAT AFTER LNDG EXIT AT TAXIWAY ECHO IF UNABLE THEN EXIT AT THE END. APCH SPD WAS NORMAL AND WE LANDED IN THE TOUCHDOWN ZONE. I SLOWED THE ACFT TO APPROX 30 KTS AT TAXIWAY ECHO BUT I DID NOT FEEL COMFORTABLE MAKING THE TURN AT THAT SPD. WE CONTINUED OUR TAXI TOWARD THE END. BOSTON TWR INSTRUCTED US TO EXPEDITE TO THE END TFC ON A 1/2 MI FINAL. AS WE APCHED THE STOPWAY NO FURTHER INSTRUCTIONS WERE ISSUED. I SLOWED APCHING THE LAST TAXIWAY; THE TWR INSTRUCTED US TO TURN R. AFTER EXITING THE RWY I WAS INSTRUCTED TO CALL THE TWR. I WAS THEN INFORMED THAT I WAS NOT SUPPOSED TO TAXI ONTO THE STOPWAY. I TOLD THE AREA MGR THAT THE CTLR INSTRUCTED ME TO TAXI TO THE END AND TURN OFF. THAT CLRNC AUTHORIZED ME TO OPERATE ON THE STOPWAY. REF 10-9 BOS AND COMPANY FLT MANUAL BOS. THE STOPWAY HAS INTERSECTING RWYS AND TAXIWAYS FOR USE BY ACFT WHEN AUTHORIZED BY THE CTL TWR. THE TWR MGR THEN SAID WE MAY HAVE LED YOU INTO THIS. WE DID EXACTLY WHAT WE WERE TOLD TO DO BY THE TWR. IF THE TWR DID NOT WANT US TO OPERATE ON THE STOPWAY THEN A BETTER CLRNC WOULD HAVE BEEN IF UNABLE TAXIWAY ECHO THEN EXIT AT SIERRA SHORT OF THE STOPWAY. DON'T SAY EXIT AT THE END; BECAUSE THE STOPWAY IS THE SAME WIDTH AS THE RWY AND IT HAS INTERSECTING RWYS AND TAXIWAYS. INSIDE THE FINAL APCH FIX AND DURING LNDG ROLLOUT IS NOT A GOOD TIME TO ISSUE FURTHER RESTRICTIVE ATC INSTRUCTIONS BECAUSE THE FLC IS CONCENTRATING ON MAKING CALLOUTS AND SAFELY STOPPING THE ACFT. IF A CTLR WANTED AN ACFT TO EXIT THE RWY AS SOON AS POSSIBLE THEN FOLLOW THE TAXIING ACFT DOWN THE RWY AND INSTRUCT IT TO TURN OFF AT THE NEXT INTXN.