You have this posted in the gen two forum and you have a gen three, but I will try to answer.
Your original problem as I read your posts was pinging. There are several things I know of that could cause pinging. Timing, over heating, running lean, carbon buildup, octane (that shouldn't be a problem since it should run on 87 octane just fine).
You did say the code thrown by the CEL light indicated lean, so that would be where I would start. Never having had this problem, but having read posts of those who have it could be an intake gasket problem.
Now to the rough running problem. Anytime I do some work on the engine and it runs worse than before I have to assume it's something I did causing it or a faulty part I put in.
You stated you changed the plugs and wires on the drivers side and that was when it started running rough. IMO it has to be either a faulty plug (yes I got one once) or plug wire or you have crossed the wires or knocked something loose. The plugs are difficult to get too and you may have knocked something loose without knowing it.
Changing the plugs on the passenger side is no picnic, but possible by going through the wheel well. A set of wobble extensions makes the job easier.
I just changed the plugs in mine since the local garage wanted $55 labor to do it. God only knows what Ford would charge.