Looks like about 1 in 10 starts, I'll get a cylinder 5 misfire and flashing CEL. It will idle, but rough, as expected with a misfire.
Shutting down and restarting after a couple minutes seems to be the easy workaround: so far, after a round of that, it takes a few more spins to catch than normal, but then runs fine.
Left it running to pop the hood last time, forgetting the engine is covered so I can't just directly start tapping on the coil and injector or jiggling the wire, and by the time I was wondering whether to leave it running while getting the cover off, it just smoothed right out and idled normally.
Hasn't done it while driving yet, only at startup. Cold or hot start doesn't seem to matter, as I've had it happen at both.
I've swapped the 5 and 6 plug and coil to see if it follows to 6 or stays on 5, but of course it ran fine each restart since. Really no visual difference between the plugs, though 5's gap may have been a few thou bigger. (I think my gap gauge is buried somewhere in the back of my 02 Focus among other random tools, and it's too hot to go dig for it right now.)

Anybody seen this?

Also, is there any real reason to put the plastic cover back on, or is this one purely aesthetic? Not planning to toss it, but if there's no other benefit, I might as well leave it off until I get this figured out.

 

I used to suggest switching coils to pin down a cause for a misfire, but not anymore.

Why ?
If the coil is shorted and has damaged the driver in the PCM, moving it to another position can damage another driver in the PCM and now you could wind up with 2 misfires, plus a damaged PCM, so not recommended to switch coils with a different cyl .