In my experience, misfires with Coil On Plug engines is 99% of the time related to a bad coil and it's not totally unheard of to get bad coils out of the box or shortly after installation.
I've replaced all the coils in my wife's '03 SL a couple of times (at least). I ran some 8 gauge wire from the ground terminal of the battery directly to the engine and haven't had any go since then.
I used to own a '97 Taurus SHO (V8) with COPs and it had the same problem. It would misfire intermittently but not bad enough to set a code. It was always a coil, not a plug or injector.
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