I would start with plug wires before anything else.
the 4.6's were very sensitive on what kind of wires that they had on them, and if they get old etc.
See if it has the original wires on it or if they are aftermarket, I would put motorcraft wires back on it and go from there.
I've own several 4.6's with the 2 coil system mounted one on each side and haven't ever had one go bad so I would firstly start with the wires.
the 4.6's were very sensitive on what kind of wires that they had on them, and if they get old etc.
See if it has the original wires on it or if they are aftermarket, I would put motorcraft wires back on it and go from there.
I've own several 4.6's with the 2 coil system mounted one on each side and haven't ever had one go bad so I would firstly start with the wires.