One of four things:
1-Bad stator (alternator as you call it)
Dissconnect the Stator plug and check for proper resistatce across the phases (for '07 and older it is three phase, '08 and new 1 phase). I can't remember the resitance off the top of my head, but I think it should be between 0.5 and 1.0 ohm.
2-Bad regulator
If the stator is good check the voltage output of the regulator to the battery when the bike is running with the engine reved up a bit (to like 3.5k rpm). Should read between 13 and 14 volts.
3-Bad battery
Do a google seach on how to test a battery
4-Leakage current when bike is sitting
Disconnect one of the leads from the battery. Place a multimeter into current measure mode and place one lead on the battery and the other on the the disconnted lead. You should see no current draw. If there is you are leaking current when the bike is off (all the way off no lights nothing), that is what is killing your battery.
My guess from what you're saying points a 3 or 4, most likely 3 if you have had your mods installed with no issue before, but check all of these. Also, when its good practice to replace the stator and regulator as a pair, its an expensive bullet to bite, but it can save you from frying a brand new stator or regulator with the other bad part.
