Joe,
Not to question your skills or anything but are you 100% positive you have
no spark? My first guess would have been a fuel pump problem (which cougars
are known for) or you fuel shutoff switch has been tripped.  Since you have
spark then I would be looking at the iginition control module or the
connections to it.  Since the engine cranks it rules out the anti theft
device because the engine would not even crank if the key was not programmed
properly for the car.  I also suggest something along the lines of a crank
position sensor (if equipped..not sure) or something of that nature that
would relay to the computer the car is in a starting sequence.  My final
thought would be the computer itself but I hope for your sake that it is not
since I hear that they are pretty expensive. I admit I am not sure if any of
these problems would generate a code on a OBDII scanner but I hope my 2
cents helps.  By the way I own a 99 cougar as well so please post the
solution to this problem if you find it and good luck!

Dana