Rough run at idle and sometimes stumbles on acceleration

I was a mechanic for over forty years, now retired and seventy five I do not know much about these newer cars.
This car has a rough idle and sometimes stumbles on acceleration, once popped back through intake and almost stalled.
What I have done so far is I found the battery ground cable was not connected to the engine and must not have been since new as there has never been any work done on this car until now. I connected the cable, the only ground has been the smaller wire going to the inner fender panel and it was loose, I wonder how the car ever started or ran like this.

I replaced the plugs and wires, the egr valve and egr tube, the pcv valve and elbow, intake plenum oring seals, fuel filter and used seafoam in the tank with premium fuel. The car runs worse now than before even after all this done.

I bought the FIXD module and it gave me two codes when the check engine light was on P0303 number three misfire misfire and code P0316 misfire detected first 1000 revolutions on startup. This was before I found the ground wire off so I connected the ground wire and cleared the codes and so far no new codes or CEL.

Could that ground wire being off done damage to any part of the electrical system?

Thanks for your help.