Later in his career, Borkowski returned full-time to driving sports GT and prototype race cars in the Rolex Sports Car Series. In 2003, he was hired by legendary Brumos Racing to campaign a Porsche powered Daytona Prototype alongside David Donohue in the inaugural season for the Rolex Series and Daytona Prototype class. Together Borkowski and Donohue won three races, stood on the podium ten times, and finished second overall in the series championship. Between 2003 and 2010, Borkowski competed in both the Rolex Series' Daytona Prototype and GT classes for various teams including Speedsource, Michael Shank Racing, Playboy Racing, and Stevenson Motorsports. During this period he drove a variety of cars with a variety of co-drivers including Daytona Prototype's (with Paul Tracy, Kenny Wilden, and Brian Friselle), a Nissan 350Z and BMW M6 (with Tommy Constantine), and a Chevrolet Camaro GT.R (with Matt Bell).