You're right to be concerned. I paid $1500 for it, three times that to have the misfire issue "fixed" (among a bunch of other delayed maintenance), and after the misfire came back I gave up. I've been driving it on 5 cylinders for years now.
If only I could find an "open loop" switch to just disable the engine monitoring. Everything runs fine in open loop mode.
That's an interesting puzzle. If you want my $0.02 cents on it check the knock sensor or unplug it for a bit and see what that does, alternatively replace ignition coil for that cylinder, cable, cap and plug.
Those would by my main suspects if it works well in open loop mode, knock sensor first.
If it runs fine in open loop mode, it sounds likely to be a bad knock sensor causing the ecu to think there's detonation and retard the timing to the point it doesn't fire at all. As far as getting it into open loop mode, unplugging the throttle position sensor or any of the other intake sensors (MAP, Mass airflow, etc) would probably get you there.
If only I could find an "open loop" switch to just disable the engine monitoring. Everything runs fine in open loop mode.