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You said you used a fire extinguisher on the battery fire.
If it was a Dry Chemical type you may have created a bigger problem for yourself.
The chemicals in a Dry Chemical extinguisher are very corrosive to electrical components/connections. I would recommend that you remove every bit of the chemical from any connections it may have got on or in. Best way would be to use high pressure air to blow it out. Then I would wash the connection with clean water and use high pressure air again to dry it out.
I got two bad batteries in a row from Advance Auto, they tested them and found they were bad themselves, the second one only made it sixty miles until it failed.
I thought it was a regulator, original 98 so it made sense and I called Cycle Electric. The tech I got there told me he suspected I was buying cheep Chinese made batteries from a chain auto parts store, which was true, and suggested I go with an American made battery and that my regulator was probably fine.
I got a Big Crank battery at Battery Mart and my problem was solved, which sure sounds a lot like the problem you are having.
I also, after many miles of problem free riding after that, ordered a Cycle Electric low voltage regulator as insurance against a old regulator failure and because I was so impressed with the service I had received from those guys and the accuracy of their diagnosis.
Just throwing that out there and I'm certainly no expert.
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