1969 was a fascinating year in the Trans-Am, and one I've studied in detail over the years. Ford ran four factory Mustangs, two by Bud Moore Engineering, and two by Shelby. In later races, a fifth car was added! By contrast, Penske ran just two Camaros, for Mark Donohue and Ronnie Bucknum. In fact, Penske only had two cars! There were no backup cars. When things began to get heated as the season wore on, they were advised to get themselves a back-up car, in the event one of the Ford guys sacrificed their car to eliminate Donohue, so they purchased back one of their old 1968 cars.
Ford were very fast in the early rounds, particularly the Bud Moore cars. By now, Shelby was on the outer with Ford. The Moore cars ran Firestone tyres, the Shelby cars ran Goodyears. But the Firestones were faster.
It was the big shunts in a couple of the early races that really set Ford back though, because they had to switch their resources from developing their cars to go faster, to building completely new cars. This put them on the back foot and they never caught up. Penske went on to win the championship for Chevrolet. There was no Drivers championship in 1969, but if there was, Donohue would have been champion.