I have the same problem with my 2008 CBR 1000 I had the worse luck it turned out that the batteries were all faulty make sure it is the right amps and that you do not have anything that runs all the time on the battery while the bike is not running.
assuming the new stator and reg/rec is installed correctly and everything is charging fine, i would then look for points of excessive resistance. cooroded connectors, shorts, and other things of that nature will drain your battery. these charging systems are only 350 watts, which isnt much.
also, if the bike was laid down at some point, its not uncommon for the rotors to get damaged. broken magnets can frw rec recs pretty quick, not to mention the possibility of the rotor hitting the stator and bending the lams into the wire
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