I'm having a really hard time following the path of troubleshooting and repair in this thread. It started with a misfire (and misfire code) under load and we were thinking a bad coil but then it turned out that the PCM has been repaired and might be bad again. Now it idles well, but stumbles and hesitates at low RPM but smooths out under load. No apparent vacuum leak and good fuel trims, so you're replacing motor mounts...??
What about the bad coil? What about the PCM? (in the last year, I have known several Ford owners, including myself, with bad PCMs, weird) Any thoughts as to why the original problem went away (?) and you have a different problem now?
With reason - were I to give this thread a new title, it might be something like "2007 Ford Fusion 3.0 - A Study In Scope Creep" or "Down The Rabbit Hole With A 2007 Fusion".
You've pretty much got the sequence of events correct - I'll provide a bit more history. A few weeks ago a friend mentioned that his car would go dead after sitting for a few days. I offered to check the dark current and battery health.
He brought the car over, and I checked the dark current (c. 25 mA - pretty normal) and load-tested the battery (which stayed in the green, so passed fine), and told him to drive it more often or buy a trickle charger.
He mentioned there was also a CEL. I read it (P0302 - misfire on #2) and cleared it. Cylinder #2 is on the rear bank, and it's necessary to pull the IM to access the plug and coil, so I didn't check the #2 plug. I did pull #5 (middle plug on the front bank) and it looked fine. (I wanted to get a feeling for the state of the plugs.)
He put me in touch with his son who told me about a bad coil killing a diode in the ECM at some point in the past. Son said the damage was apparent once one opened the ECM. That had also caused a P0302.
My friend brought the car back, and my plan was to pull the ECM and do a visual inspection. However, the CEL had still not triggered again. My friend had mentioned that flooring it and winding up the revs a bit will trigger the CEL.
I took the car for a drive (had not driven it previously), and noticed it idled roughly and lurched and jerked badly at low speed. There was a bad lag under acceleration, but after the revs got up, it ran fine. Steady-state cruising was fine. No CEL, although I would have fully expected one based on how rough it was at low speeds.
OK, so running poorly with no CEL? Time to do some research.
The first thing I tried was an idle relearn, which I should have done, but didn't know about, after I had disconnected the -ve battery terminal for the dark current test.
The relearn brought the idle up, and the engine was now fine at idle in Park. (Thanks, Fusion forums!) However, it was still pretty rough in D, though not as bad as before the idle relearn.
The other thing that kept coming up on the forums was that if the idle was acceptable in P but poor in D, a likely cause was a worn "dog bone" torsion strut. I had my wife start the car and shift into D while I watched the engine compartment, and was a bit surprised to see the engine lurch quite a few degrees.
Today I got the exhaust pipe removed (broke an exhaust manifold flange stud, which I had to drill out) and was then able to remove the dog bone.
Poor design - they could have easily made it such that the exhaust system did not block the dog bone bolts.
