Charging problem replaced bat and voltage reg, at start up voltage 12.50 dc, after 20 min run time voltage dropes to 11.50 dc. on a 2 to 3 hr trip bat will not start bike, bat will charge back to normal

so check and test battery and cables

check for a missing wire to the battery as the voltage regulators are not controlling anything
if you have a 32 amp alternator and it is producing 48 amps , the voltage regulator is not controlling the out put of the stator so it will burn out from overload
voltage from the stator has to be 13.2 volts DC minimum and no more than 14.5 v DC at 2,000rpms
suggest that you get an accredited bike electrician to check out the circuits and system

It sounds like you have something that is drawing some power off of it while it is turned off. You will need to track down this parasitic drain or disconnect the battery each time you park it.

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Lisa I'M sorry to say their isn't any fuse or fuses that can correct problems with our alterator.Their is what is called a fuseable line witch is basicaly reistance wire that will burn out if over loaded .However you would have nothing even with a new battery NO CRANKING.
The ALT .uses diodes it is AC alternating currant unlike DC direct current..The diodes olny allow the currant to flow in 1 derection and uses a voltage regulator to allow the systems that are DC the battery to charge and at the same time other systems that run on AC voltage to work as well .
Your best bet is to talk it to somebody who you trust and test what you get at the battery with the vehicle running if it reads 14 volts at the top of the battery DC then the ALT IS GOOD , Check the BAT , at this point with the NEGITIVE cable off the BAT. It should read at least 12 volts DC on a 20 volt Dc scale.
But likely it is the alternator

It's normal for the reg to heat up this I'd how they reduce the current from AC to DC and convert the excess voltage to heat. You need to test your charging rate with a multi-metre set it to 20 DC Volts you should get between 13.5 V to 14 V if it is above 14 there is z problem that needs sorting possibly need to replace the reg. Regards Jim.

amps or volts
11 to 12 amps indicates nothing but if it is volts then it indicates that the alternator is not charging the battery
Battery voltage is 12 -13.5 volts and when charging is 14.5-14.8 volts dc
the rest of your statement indicates that the alternator or voltage regulator is faulty and you should have the charging system checked by an accredited auto electrician

W running measure voltage at bat w/ vom should be 13.5 V 200 rpm 14.2 V ..good charged bat not running will be 12.65 V If u aint getting these voltages running could be reg is bad or stator ...good luck good help I found also harleytalking.con.....

Never take the cable off when running. Its so hard on the voltage reg. And the alternator. Take the alternator and get it tested free at auto-zone or O rilleys. they test mine free all the time. Hope this is helpfull .. Sawdust46

your voltage/reg. can be tested in a couple different ways check ground res. check res. then revs. bias on diodes you have ac in dc out it sounds like you may have a diode gone bad allowing ac curent to flow causing the wires to get hot

well , the ECU runs the alternator. (DG wire "dark green")
the alternator field is controlled 100% by PCM reg , inside PCM.
so..... if the running engine has 13.3, to 15vdc the alt is working
if lower, its not. (rpm on engine 800 or more)

not scanning the PCM a the CEL glow, you missed the boat.
why not scan it. see why the PCM is upset (DTC errors stored)

see the 2 lower pins below , those go to PCM.
in theory if the field in the old BAD ALT, was shorted.
that could in fact, burn up the PCM regulator.
shorting outputs of PCM , does that in most cases.
im the poor sod that fixes PCM's.so....