computer flash?

I just had my 99 windstar's 3.8 engine replaced by a local garage, it keeps coming up w/ 1309 code, after taking it back multiple times the mechanic thinks the computer has to be flashed by the dealer being that its the original computer and a used engine. The camshaft pos. sensor, is new, installed correctly, and functioning correctly. does this sound right to anybody??? especially that he wants me to pay for it after paying $2600 for the motor and installation.

That code is caused by either a faulty CMP sensor or the sensor is not syncronized.

Verify the CMP is installed correctly and not out of synchronization (timing).