5 ohm coils if you do much city driving. If all you do is highway driving or keep the engine above 3000 all the time, then the 3 ohm is tolerable.
But, know that idling WILL deplete the battery and the more load you place on it the faster it depletes.
Stock coils are 4.7 to 5 ohm, and they worked pretty well since 74, no?
Stock plug wires are metal core. The core last longer than most humans and are unlikely to be "hinky". The jacket insulation, not so much. If not cracked, they still wok fine. There should be resistance in the ignition path. Spark plug caps/boots had that resistance from the factory. Graphite wires have built in resistance, break down with time and must be replaced frequently (compared to metal core.) You'll have to decide where you want to put the resistance, in the wires, in the plug boots, or in the plugs. Choose only one place.
Your muffler is probably too restrictive, particularly if it is quiet. But, read the spark plug deposits for better info about how it has effected mixture.
A new air filter is required replacement every year if it is paper type. I don't care how it looks. The paper collapses in on itself, and it can never be cleaned thoroughly.
You could try a test without the filter element just to see what effect it has.
Anyway, addressing all performance issues begins with thoroughly completing the entire routine 3000 mile tune up checklist.
Cheers,