A G-1159 FO RPTED THAT HE WAS IN THE L SEAT; TAXIING; AND THAT HE INCURRED ON RWY 25R AT MKE.

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ON GND TAXI FROM THE FBO WITH THE FO IN THE L SEAT AND THE CAPT IN THE R SEAT. RECEIVED TAXI CLRNC AND CALLED GND BACK TO CLARIFY THE TAXI CLRNC. TAXI CLRNC WAS REISSUED INCLUDING INSTRUCTIONS TO HOLD SHORT OF RWY 25R. AFTER TAXI CLRNC WAS READ BACK; THE CREW ASKED FOR RWY 19. THE GND CTLR SAID THE COUNTY WOULD HAVE TO BE NOTIFIED AND WOULD INCLUDE A 15 MIN DELAY. GND CTLR READ TAXI CLRNC TO FOLLOW TXWY F; TURN R AND TAXI DOWN THE PARALLEL. IN NONE OF THE FOLLOWING XMISSIONS FROM GND DOES EITHER PLT RECALL ANY HOLD SHORT INSTRUCTIONS. ATC CALLED THE ACFT AND SAID 'STOP.' I STOPPED; WITH THE NOSE SHORT OF THE N BOUNDARY LINE OF RWY 25R. AT THE TIME THE INCIDENT OCCURRED; A TWIN BEECH WAS TAKING OFF ON RWY 25R. AFTER THE ACFT WAS STOPPED; GND WAS CALLED NUMEROUS TIMES WITH NO RESPONSE. A CONTRIBUTING FACTOR TO THIS SIT WAS THE CONFUSING TAXI CLRNC. ADDITIONALLY; AFTER THE REQUEST WAS MADE FOR AN ALTERNATE RWY; THE HOLD SHORT INSTRUCTIONS SHOULD HAVE BEEN REPEATED WHEN THE TAXI CLRNC WAS READ TO US FOR CLARIFICATION PURPOSES.