Use an OHM meter to check resistance on the plug wires. I honestly don't know what the spec is, but if one is far off from any others, that could be your problem.
My #2 went bad and I couldn't tell until I had swapped it out with one I got from the yard and the car ran better (not great, but better). These can be tested regardless of valve cover installation.
Hell I figured it out which one was the problem when I unplugged it while the engine was running and noticed #2 removed didn't cause the car to run any worse!
I doubt you have a coil issue, possible, but unlikely. I have no idea how to test it wouth having an extra pack. I now have 2 laying around the garage.
Perhaps the fuel filter is clogged, that could cause lean conditions and lead to misfiring. If you happen to fill up just after the truck that refilled the tanks pulled out you can get a lot of the dirt and junk that was stirred up.
Since you still have the valve cover off, I'd get the motor to TDC. IIRC there is a way to stick a bolt through an access hole at the back of the block and lock the motor at TDC. From there you can check the cams are timed correctly. I honestly don't recall what the marks look like. It's been 6 years since I've tore open one of these.
I put the valve cover back on. Started the car. Pulled spark plug wire from cylinder 1. No change in crappy idle. This wire was also sparking any time it got near metal.
I pulled wires from all the other cylinders one at a time. Engine ran much worse each time. Also none of these wires sparked when placed near metal.
So I have a problem either with the coil or the spark plug wire for cylinder #4. I looked in the tube that goes over the spark plug and it was filled with oil and a lot of gunk, while the others were clean. I cleaned it out with qtips as best I could, put it back on, and it ran noticeably better, but still misses pretty good.
Right now I'm not sure if it is a bad wire, a bad coil, or both. I think it's weird that only the wire in question sparked when near metal and the others didn't. Could the coil be shorting out or did my wire take a crap? Best price I can find on a new set of wires is $100, where a new coil is $50
What do you think is bad? Coil or wire?