1998 Ford Contour code

Hi Fadi
let me see if I get what you are saying
check engine light on
car was running but you have check engine light on
disconnected battery
and know it will not start
does it crank (engine turn but will not start )
let me know so we can solve this

You can not clear the PCM so its not functional
when you disconnect the battery you are clearing the codes but PCM will retain all programming software
and you need to hook it up to a computer and need software from ford to reprogram it
it the PCM was not changed than all car info should be in it
again what is the issue that happening making you think that the PCM need to be reprogrammed
does the engine crank?
Have you check the security system?
Do you have security light on when trying to start
KEY PROGRAMMING - NEW KEY
Connect New Generation Star (NGS) tester to Data Link Connector (DLC). Insert unprogrammed key in ignition and turn to RUN position. Wait for theft warning indicator to go out (about 2 seconds), then flash rapidly. Select PATS module on NGS.
Select IGNITION KEY - CODE ERASE FUNCTION test (press TRIGGER twice). TEST IN PROGRESS will be displayed on screen. After 8 minutes, TEST COMPLETE will be displayed on screen. All keys are now erased. Turn key off, then to RUN position. Wait for theft warning indicator to go out (about 2 seconds). PATS key is now programmed. To program additional keys, see KEY PROGRAMMING - SPARE KEY.
KEY PROGRAMMING - SPARE KEY
Cycle ignition switch from LOCK to ON position 3 times with a programmed key. Within 5 seconds, insert a new PATS key into ignition and turn it to ON or START position. Theft warning indicator should light for 2 seconds and vehicle can be started. Repeat this procedure to program additional keys.