Just in case change the plugs and check that all leads are making contact with the plugs.it can be so simple you could miss it! You can send it to the nearest auto repair shop in your town.

Most of thease new engines have a place to unplug the injector harness from the car for engine removal. locate that plug --- unplug it and plug it back in --- disconnect the battery for 20 minutes and then connect it up again and go for a drive. (it could be as simple as that). Other than that -- now you begin to see why auto repair is exspensive. so if reseting the pcm didn't do the trick the do the following - yea its a pain - but unless you have ten grand to spend on a diagnostic tool--- this will do.

Ford uses a ground switched fuel injector signal. so with the key on unplug the injector and using a test probe, make sure all injectors have power to the positive pin (you'll know because the light will come on) if it does have power to all the injectors, then it may be a grounding problem, so switch your power probe to the positive post on your battery and check them all again (you already hve them all unplugged now anyway) if your test probe lights up --THEN THAT is the injector giving you problems - because the injector's ground wire is grounded constantly causeing the injector to inject fuel constantly.
    to findout watch injector is Not firing --- start engine and unplug them one at a time, if engine does NOT stumble worse than it already is when you unplug the injector -- then that is the injector that is not working ----- that does NOT mean you really have a bad injector though - do the test above and if it doesnt check out then check the wires all the way back to the PCM Power control modual. If they are ok -- you better clean your battery posts and all grounds and --- make sure your battery is up to snuff and that the alternator is actually charging. (low battery voltage hinders injector preformance)

thank you for the tip.  I changed the pickup  and  the module but it didnt fix it. the timing is good so i think it is in the fuel system. any ideas how to pinpoint a bad fuel injector when half of engine is covered by the intake plenum?any advice would be apreciated thanks

89 mustang gt 5.0 it idles good starts every time. but it misses when driving from 1 gear through 4th it is automatic.after checking all basics tune up parts and fuel system all good and new. i decided to change the pick up in the distributor since it has 170000 miles on it. how do i remove the timing gear from the bottom of the distributor?