1. It has to have a misfire for atless 2 cycles, but if it had a constant misfire in a cylinder it would probably turn on right away.
2. Nope
3 ? My state we use a OBD2 connection to test 96+ which just reinsures the check engine light isn't on and it has gone threw a few drive cycles. With 2 speed idle tests just letting the car heat up for a bit before testing will sometimes allow it to do better and pass.
I would replace wires, cap and rotor with plugs. Wires are like 50 bucks cap and rotor are like 20. It is just apart of tuning it up. If it is still misfiring I would look at the injectors.
Do you know how tight to tighten a spark plug? Sometimes misfires come from not tightening a spark plug enough. People are typically scared of breaking one off, thank god I haven't ever broke one. To install a spark plug first you line the treads up using just the extention. Once lined up tighten until the pressure you are applying changes. This is where you want to pay attention. Continue to turn with this same pressure until the plug hits a spot where the pressure needed to turn increases again and that is how tight you want them.