Hi Craig,

The ECU monitors the crankspeed for each cylinders contribution.

The ECU control on your vehicle will shut off the injector on any cylinder that is contributing less than the others (incomplete burn) this is to prolong the life of the CAT and reduce emissions.

Im sure somebody will correct me if I am wrong.

Scope the injector current on the offending cylinder or scope them all at the fuse when the code is there and then clear the code.

I have had a few different outcomes with similar symptoms as yours.

A couple with leaking/burnt out exhaust valves.
Ignition issues/weak secondary.
and
1 injector issue.

Can you monitor the misfire counters?

Check the emissions.

Check cylinder leakage, hot and cold.

On this engine I sometimes stick my borescope down the plug hole and with some cotton tied to the end pull the camera is a position so you can inspect the valves.

hope that helps

cheers
James