in trying to figure this out my friend has a 1999 mustang 4.6l 5 speed manual trans. from time to time it would not start just crank. leave it for a few days hit the key it would start. This time i notice that the theft light blink when im crankling it over. do not recall seeing this before. tryed disarming it by following the book does not work. Is this why it won't start because the theft light is blinking. When the theft light blinks you can here the fuel pump for a split second that it.

Thanks

 

My friend also has the smiliar problem with you and he take it to auto service and everything is good now. i will ask to him and will let you know soon.