The main battery charge was at bottom bar from sitting . Car would only run rough in neutral. After 5 minutes it ran in park and now charge is at second bar. Still runs rough and shuts off as if charged. Will restart with accelerator pushed but still shows half charged. Will driving charge to full ?
Short answer, yes, provided other systems are up to spec. By design, the Classic HV SOC is typically between 60-80%, IIRC. The indicator on my 2002 has never exceeded the 3/4 full mark.
Ok good .. it is currently misfiring on cyl 2 &4. Has new plugs and coils. Law main cause this misfiring?
No. Look for usual rough-running engine causes. The gas engine is no different in a Prius than other gas engines.
I suggest that you do a simple process that is called "force charging". It is harmless to your car and drive system and could help at kicking your battery back to life. Put the parking brake on. Press your left foot down firmly on the brake pedal. Push the accelerator down to the floor. Stay with that and watch the charge box start rising up in bars. Keep going till all bars are completely full. Drive normally for a while and watch how the charge box/meter reads. It should eventually make its way down into the bottom third of the meter then charge up to around the 80% region of and on and that is normal. It won't, or shouldn't charge up to 100% in normal operation, unless you are regenerative charging down a very long hill or are parked and "force charging" it. If the meter goes up to 100% quickly or drops to one bar while under normal operation, you might have a weaken battery and might need a few replacement cells or so. But if your battery drops to one or two bars again, don't panic yet. Just re-do the force charge process again and see how it does while driving again. You might need to do this a few times. If after a few of these force charge cycles the battery does not perform properly, it is time to look at a good diagnosis and servicing of your battery. If you've got money to throw at it, go ahead and buy a new or refurbished battery assembly. Personally, I am a strong advocate for RECYCLE/RESTORE/REUSE, and these batteries are perfectly capable of that, and I strongly believe that it is the Ecological and Social Economical Right Thing To Do. And I and my 2003 Prius Gen 1 with 244k mile on the original battery assembly with 93% estimated lifetime reading, have thrived doing thing this way. I hope that force charging helps you out. Let me know.
If you are having misfires and other running conditions with the engine it is more than likely not caused by the Hybrid Battery, but it could well be the cause of your battery running down. With a misfiring or improperly running engine that is probably not starting and shutting down during operation properly, there is more demand on your electric drive system and in turn more stress on the battery. A bad running engine id a Hybrid Battery killer.