From a USA Today article:
"Pilot Lt. Cmdr. David Faehnle and radar intercept officer Lt. Cmdr. Robert Gentry gave a final salute from inside their cockpit before aircraft 102 taxied down the runway and out of sight at Oceana Naval Air Station. The plane that actually took off as thousands applauded and whistled, however, was aircraft 107, with Lt. Cmdr. Chris Richard at the controls and intercept officer Lt. Mike Petronis in the back seat.
The first jet had mechanical problems — “a common occurrence with the F-14,” said Mike Maus, a Navy spokesman. The second jet had been on standby just in case."
I suppose that’s a good a reason as any for making the change.