Please, can someone tell me if the motor out of a '99 F150 4x2 will fit into my '97 F150 4x4 4.6L (Windsor). I blew the head gasket, (I hope thats all) and I found a wrecked truck with a good motor. Any help would be appreciated.

 

U might like this link.

Decided just to rebuild the entire engine *pics* - Crownvic.net

 

I think the 4.6 eng are the same but the 97 has coil packs & the 99 has a coil on plug set up. I also have read the cop set up can be modified to operate on the coil pack ecm in your 97. Unless that's your cup of tea I would just use the coil packs.
you might need to change to the 97 Intake as the fuel system is a return set up I'm not sure about the 99 if it is a return style your good.

 

Like others have said swap the plug wire with another to see if the misfire moves I think you may not be seating the wire on the plug. Are they factory ford wires?