Totally discharging a battery is bad for the battery. You could have it charged then tested to see how much life is left in it. If it is more than 3-4 years old it probably needs replacing.
As far as the alternator, many automotive stores like Autozone will test it for free.
The other thing to do is, with the battery charged have the parasitic draw checked, ie how many amps are being used when the vehicle is off, after the work you did there might be something drawing the battery down.