If it just happened like that then it's possible the plugs just got jarred loose during all of the other repairs. I've had both UVCHs (Under Valve Cover Harnesses) in my truck, but the rough running was progressive and could be detected with a Cylinder Contribution Test.
There is no code for "valve cover gasket" but if that entire bank of injectors suddenly quit firing properly and all of the even numbered injectors are failing a buzz test and/or cylinder contribution test that is a very likely culprit.
"The head gaskets were checked" could put the mechanic in the vicinity of the UVCH plugs. They do become brittle with age and perhaps they got broke, disconnected, or something along those lines.
The left side is the easier of the two, I can do mine start to finish in an hour or so.
