Did I finally kill my FJR?

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Keep in mind that there is a big difference between a battery charger and a maintenance charger. A good maintenance charger will only charge the battery when it drops below a threshold and just monitor it the rest of the time. Really good maintenance chargers will test and desulfate the battery when needed as well. Optimate III is my favorite and has been since around '05 when I got my first one for the '04 FJR. They often sell them cheaper as Honda branded units, so it pays to look around if you're in the market. I got 9 years from my original Yuasa battery on the FJR and it was still good when I sold it. It desulfated three times, the first time I hooked up the battery after two years of use, about 5 years later and a month or so before I sold the bike.

If you're really not going to be riding a bike for potentially years, it's probably a good idea to pull the plugs and squirt a little engine oil in the plug holes, reinstall the plugs, top off the fuel with some Stabil and just leave it alone. On the center stand if possible to take weight off the tires to a degree, and remove the battery and store it in a location not on concrete that is temperature controlled, ideally on a maintenance charger.
 
Left Yuasa in the 90s when they kept prematurely dying in the TX summers. Went to WalMart for (something after that). The GL1500 was always happiest when swapping batteries every 2.5 years (if I didn't want to end up hunting price-hiked batteries in some remote village). But never went back to Yuasa after.
 
Yuasa is your best bet. I had one last 8 plus years in my Gold Wing but 5 years plus is not uncommon. I've read that it's a good idea not to leave a tender on your battery 24/7 for months on end but rather every 3 weeks turn off the tender and just let the battery "rest" for a week before turning on the tender back on.
Riding it once a month would be real helpful too.
Helpful for both bike and rider!
 
and store it in a location not on concrete
Storing a battery on a concrete floor will not harm it in any way. The hard plastic case is non-conductive and will not discharge, absorb moisture or release acid. This may have applied to much older battery generations... It is, however, a good idea to keep the top of the battery clean (salts, dirt or acid residues) and protect the terminals from accidental contact with anything that might cause a short circuit.

It is best to store the battery fully charged, especially if storage location gets very cold - freezing point for a fully charged battery is much lower than one that is discharged. Personally, I never use a battery tender and don't normally disconnect the battery from the bike although using a properly functioning tender or maintainer (not trickle charger) won't hurt anything. Unlike some battery chemistries, lead-acid and AGM batteries "like" to be kept fully charged. They also don't "like" to be deep-discharged or "cycled" although some types are designed to be more tolerant of cycling.

A modern AGM battery in good condition has a very low self-discharge rate (a few percent per month) and the FJR has a very low parasitic draw. To be safe, I will do a top-off charge maybe twice over a four month layoff using a one amp charger for a few hours.
(Current OEM Yuasa battery in my 2011 is almost 12 years old and has around 100,000 miles on it...)
 
As far as my not on concrete comment goes, it's more for temperature changes than discharge, imho. Temp controlled environment will help when you're talking long term of months or years.
 

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