I had the truck put on the monitor to see what the code was when it was missing. The dealer said it showed #3 so we replaced the 3rd plug and coil. after that he reset the code and 20 minutes later it started missing again and the engine lite came on.
If you are going to replace none plug, replace them all, you get that doubt out of the way. It could be another Coil, take it back to the dealer, for another code check.
I don’t know what engine we are talking about but the 4.0 liter has 6 coils, at least mine does.
You need to have the codes read again. Some places will read them for FREE. Try Autozone or Advanced Auto Parts. Get the exact code not just their translation into English and post it back here.
The computers on modern cars continuously monitors the speed of the crankshaft. If reads the speed change that each cylinder firing produces. If it sees a consistent lack of contribution from cylinder #3 it sets the code and turns on the CEL.
Now that cylinder may be misfiring for a number of reasons. It could be an ignition problem (you have looked at that); a charge retention problem (compression – rings, head gasket, piston, valves); a mixture problem (injector rich or lean, manifold air leak, air leak at a valve stem); etc. The mechanic has to analyze #3 as if it were working independent of all the others and find out what specifically is wrong that particular one. This is going to an interesting trouble shooting problem.