Down to 12.21? Ouch that is very low, when my alternator acts up my battery gets that low and it is difficult to start.
you probably already know this but I going to say it anyway just in case you do not, the voltage readings as an indicator of state of charge only apply to a battery "at rest" i.e. one that has not been charged or discharged for many hours. If you charged it to 12.8 and stopped it was not fully charged. 12.8 was a surface charge not a state of charge, For instance my batteries will read upper 13v just after shut down and quickly drop, as the voltage approaches its state of charge the drop tapers and slows, in the opposite a discharge will make the voltage drop, when the load is removed the voltage reading will increase towards its state of charge. The longer it rests the more accurate the measure but you can get a decent reading in an hour or two
http://www.uuhome.de/william.darden/carfaq4.htm#measure
If you did fully charge it, and resting for 50 hours it dropped to 12.21 I agree the battery is bad, probably has an internal short. Concorde should take care of it. I have left my dome lights on for near that long, ok maybe 36 hours and granted they are LED but still the battery had plenty left to start the engine, a battery at rest with 12.21 has almost nothing left
I do not know enough about the Balmar voltage regulator to say anything with confidence.
http://www.balmar.net/PDF/2005-mc-612-manual.pdf
Looking at the unit and their description it looks pretty sweet, High accuracy user programmable logic driven voltage regulator for an alternator,
But couple problems,
In skimming that PDF They do not come out and say it but I think it is designed for an alternator with an external regulator, you could probably modify the stock alternator into a an externally regulated unit or use another alternator but that is a bit of work that is not done right gets you back where you started or worse.
Also it is quite expensive, their target customer seams to be marine applications with multiple large banks of batteries that will be heavily charged and discharged.
I am afraid it might be overkill (did I say that?) and that if you had a good working battery and alternator I think you will be happy with the stock regulation,
We may not be wringing the last 10 amp hours that our batteries are capable of with stock Toyota regulation but it should not be a problem under most circumstances.