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If it is running rich you have the wrong size jet fitted, tuning a DR650 uses jets sizes from about 130 to 180 depending what has been done to the engine & bike
i had a problem with it running hot on idle and went up 2 jet sizes from stock and it made a huge difference it also made the bike start better while hot i had to do a little tuning with that black knob you were referring to but it helped out a lot the next thing you can do is a high out put water pump or dual core radiators that will help out a lot.
1998 to 2002 have problem with plug to voltage regulator/rectifier which is under seat. connectors in plug overheat and bike stops charging the battery. you will see if connectors have been hot and will need to be replaced if they have. once replaced check bike charging with multimeter at battery,should make 13.5 - to 14.5 volts just above idle. if not will need to test stator and regulator.
sounds like you may have damaged the stator or another part of the ignition system when it shorted.
the bike will only run while the battery has power as it is not being charged when the bike is running.
when my stator went on the Harley it collapsed the battery and the bike just stopped, all the acid went over my primary cover and ruined the chrome, it was 1 week out of warranty at the time
The power from your battery goes fromt the positive post of the battery directly to the starter. At the starter, there should be two connections. The large battery cable and a smaller red wire. This red wire is "hot' wire to all the "accessories" on your bike. The wire runs straight from there to the ignition switch. If you don't have power to the main switch, you have a main fuse blown somewhere. You'll need a schematic to trace the wiring out from there. I'm sorry but I don't have a schematic for that model bike. Make sure all your connections are clean and tight and your "Run/Stop" switch in the in the proper position.
My initial thought is you haved a faulty voltage regulator. You should be charging at about 15 volts, but when your battery gets charged, the voltage regulator should turn the charge system off.
Your battery is hot ... you are over charging.
Im sorry, I dont know where your regulator is located.
Sounds like a broken fuse - or a bad electrical connection at the fuse. Try removing the fuse and carefully clean any corrosion from it and the mounting hardware. Do the same with the battery connections.
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