By the end of 1962, only two A-12s were engaged in flight tests. Full test speeds could not be reached since the J-58 engines were not fully available and were experiencing problems. CIA Director, McCone wrote to the President of United Aircraft Corporation (the parent company of Pratt & Whitney) and made a clear case by stating,
“I have been advised that the J-58 engine deliveries have been delayed again due to engine control problems. . . by the end of the year it appears we will have barely enough J-58 engines to support the flight test program adequately. . . Furthermore, due to various engine difficulties we have not yet reached design speed and altitude. Engine thrust and fuel consumption deficiencies at present prevent sustained flight at design conditions which is so necessary to complete development”.
By the end of January 1963, ten engines were available and the first flight with two J-58 engines occurred on January 15.
At speeds of Mach 2.4-2.8 the aircraft experienced such severe roughness that it was looking as if the program could not move forward. The trouble was diagnosed as being in the air inlet system of the engines. After a considerable period of experimentation the problem was solved