Hey Jess, with 118k miles it would be a very good idea to replace that fuel filter.....even if you have to take it to a dealer. Try doing it yourself again, maybe try a different type of fitting tool. The plastic ones sometimes don't do as good a job as the metal ones. You might be able to rotate the fuel tool slightly so the split contacts the "fingers" in the fuel line in a different place. There sometimes is a sweet spot that you have to hit.
If your truck is still running rough, it may be a bad coil. They sometimes become weak and it causes problems once the truck gets warm. Resistance should be between 4 and 10 kohms between the pins.
T-bird, these 5.4 engines have separate coils for each plugs. Your '99 probably had a 4.6 that has 2 coils that take care of 4 cylinders each. BTW, cool car !! | 
