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After reading through every thread I could find on the subject, and trying all suggestions, I am stumped. My 2010 1198 S Corse has a very sick charging system. It overcharges and boils batteries. I have replaced the rectifier/regulator 4 times. I just installed the fourth one (ElectroSport) and a new stator (also ElectroSport) as well as a brand new AGM battery. The last battery was a regular lead/acid type and it blew its caps and sent acid all down the side of the fairing, ruining the the beautiful Corse paint job. :( The system is still overcharging, causing the headlights and dash lights to go on and off and sometimes lighting the diags light. With a meter, I am seeing up to 16V at the battery and this is with the new battery, r/r and stator which don't even have 10 minutes of run time on them. The r/r hasn't even had a chance to get hot yet.
 

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sounds like your using the wrong regulator to me, the one to use is the one from a 999R
which is the recall part, heres a pic of what it looks like

-Carbon
 

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i use the shorai lithium cell battery and havent had problems since swapping from the stock yuasa which was a turd

-Carbon
 

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The regulator function of the regulator/rectifier (RR) is simply to limit the voltage output to avoid overcharging. If you're seeing 16 volts, the new unit was initially defective or been damaged.

A RR can be damaged by too much heat which is why a lot of owners move the RR to a cooler location on the bike. I had multiple RR failures on a 916 before I moved mine.

A RR can also be damaged by the stator wires shorting together because the insulation on the leads has been damaged by heat conducted from a loose or corroded stator-RR plug connection. Stator AC voltage output rises with rpm so a short due to insulation failure at high rpm doesn't show up on a multimeter test.

However, given that you have all new components, and given the history of the charging system failures, you can eliminate the cause as a new bad RR (it happens), so there's something else like a bad ground or electrical short that's snuffing the RR's diodes.

See attached:
 

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