Plug wires can break down, especially with heat and oil. When that happens the spark goes thru the insulation to ground, rather than to the plug. Sometimes u can find that at night by opening the hood and looking for the little lightning bolts. Resistance core wires just flat wear out with time and dont conduct well anymore. Caps and rotors can also go bad. Moisture/dirt on the inside of a cap can cause the spark to cross over to the wrong cylinder. U can attach a test tach to the engine, then pull each plug wire one at a time and watch for a change in engine rpm. If no change, then u know that cylinder is not firing.
Also, u should do a compression test. A valve/seat failure, or a broken ring, can cause very rough engine operation. Been there, done that in both cases. Both were also very low mileage parts/machine work on a rebuilt engine. NEVER assume a new part is still good, or recent machine work has not failed. Just ask Trey who refused to check his new water pump for months. (I told him to early on too) Or, ask the boys who launch the space shuttles!
Here's a spark plug failure story that was damn hard to figure out.
Back in 91 my uncle's 74 D200 was misfiring. I knew which cylinder but couldnt figure out why. The plug was as clean and pretty as new. Every time I pulled it out the gap was perfect and there was no fouling. It wasn't until I looked at it like it was in the engine that the failure was revealed. The ceramic core had broken and when the plug was right side up (electrodes down) the ceramic would slide down the center electrode and totally short out the gap! That souviner plug is sitting here on my desk to this day. Get a lot of fun handing it to guys and asking them to figure out what is wrong with it. Of course, everybody looks at a plug upside down...