Ok, let me give you the whole story. I bought a high mileage 1997 F150 with a 4.6L and 5 speed manual. It has about 200k miles on it and started misfiring on cylinder 1. So I replaced the spark plugs, coil packs and plug wires. I then found out the alternator was no good also and replaced that. Everything ran pretty well for about a month or so. I have noticed a power loss and a hesitation in acceleration during that month. Now it is misfiring on cylinder 3 and it runs like crap. Need some major help here guys. What else could be going on. My dad has a auto repair shop, but is about 80 miles away, don't want to drive it on a misfire that far. Any Ideas Please!

 

Get number 3 from a code? Check the plug for fouling. Swap that plug wire with any other and see if the misfires follows the plug wire.
Good hunting.

 

Has the throttle body been de-carboned? This is recommended at 100K miles. How about the EGR valve? Mine caused problems at 130K miles.

Good luck!