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Something is draining amps/volts on my 2002FXST. New battery (check) Charging system(check) Plugs (check) If bike is left for more than several days it won't fire. I can crank it over w/o a problem just a couple amps shy of fireing. A deep charge will get me running again.
 

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A simple experiment to determine if the Vreg is the culprit would be to unplug the Vreg, let the bike sit for a week, and see if it starts normally. If the battery still discharges then something else is draining the battery, if not, replace the Vreg.
 

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On my ’99 the only distinction that I can read (for battery/charging system) via the flashing engine check light mode is code 16, which indicates either an abnormally low or high battery reading. Not particularly useful in your case, as you already know your battery will discharge below normal use after a few days of just sitting.

However, if you threw code 16 while riding but no other problem developed shortly there after, like the battery going dead, you might deduce that there is a potential Vreg or alternator problem developing.
 

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Either the battery is going bad, the system isn't charging, or you have a current drain. What do you want to test first?
 

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The main circuit breaker is supposed to be shut. OK, if you are confident that the battery and charging system are OK, then take your multimeter and set it up to read amps on a low scale, like around 1 amp maximum, or 500 miliamps maximum, depending on your memter. Disconnect the negative terminal of the battery. Put the black lead on the cable, red lead on the battery negative terminal. Give it a couple seconds. What is the reading?
 

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new battery

can be as faulty as any other new part. You should have a actual test done to determine the new battery is in fact not the culprit. A local auto repair shop can do a load test to determine the battery is not defective. Remember if new batteries can not be defective that dealers would not need to give you a guarantee.
 
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