Knock sensor doesn't have that big of an effect on the n/a 3.3's
I just went thru something identical to this a few weeks ago.. while it's running can you smell fuel? Like its running rich. Mine was doing that.. did some research and found that the fuel pressure regulator, which is under in intake plenum and bolted to the fuel rail, can develop a hole in the diaphragm, causing extra fuel to dump into the #6 cylinder. So on a sunday I replaced the FPR and the #6 plug, reinstalled in intake plenum and fired it up.. and it ran the same.. so I drove around for 15 minutes or so to get it up to temp.. no change. I don't DD the X anymore so on monday after work I was on the way to a buddies shop to get him to plug in their scanner and run some tests. On the way there i stopped at a red light and noticed that it was idling perfect. I couldn't believe it! My buddy and I discussed it when I got there and best we can figure is that since the FPR was dumping extra fuel into the #6 cylinder, it couldn't burn it off so it went right out of the exhaust, which messed with the O2 sensors. But after driving for a while the computer realizes the conditions have changed and starts to relearn and adjust. I bet if I had driven around for longer that sunday the X would have started running better.
What I did: Pulled the fuel pump fuse and tried to start the X a few times, this releases the fuel pressure in the lines; drained the coolant, removed intake plenum, replaced fuel pressure regulator, replaced #6 spark plug, reinstalled intake plenum, and drove around for a while. It has been running fine ever since