Technically I believe the winningest Trans Am Cougar would be the Bob Estes Cougar with 6 wins in 1967 and another 6 in 1968. Those were regional wins. The Estes Cougar wore both the #77 and now is #79.
Of the Bud Moore Cougars, the #15 car had the most wins; May 30th at Lime Rock with Peter Revson driving, August 6th again with Revy driving (he had the most wins in a BME Cougar with 2) and then on September 17th at Riverside with David Pearson driving.
Gurney won on April 16th at Green Valley driving the #98 car.
Since your Cougar is a '68, the winningest Cougar driver of all time has got to be "Tiny" Lund driving for Bud Moore in the 1968 NASCAR's "Baby Grand" or GT Division with 9 wins and the championship. He drove Cougars with both the #15 and #16 that year.
According to David Tom, Team Cougar cars wore different numbers at different times. His car #98 had a unique roll bar that was very near to the bucket seat back, while the other cars (#15 & #16) had roll bars located further back (closer to the edge of the quarter window). He has pictures which identify the car that he owned wearing different numbers with different drivers, based on the roll bar location.