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Hopefully your next alternator will sort out all your problems. The most common cause of a battery draining overnight would be the alternator, if it's not that, then we need to start looking at aftermarket accessories fitted to your vehicle. Get the alternator charging first then we can worry about that.
You loose key/ignition switch is more then likely caused by a worn key, do you have a second key you can try?
From what you have posted I don't think you have any major problems with your dual battery setup, because the 2nd battery has always been able to start the vehicle.
Saying that they don't last for ever, so it might be a good idea to upgrade it.