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Hello from Canada.
It's the Best Bike Ever. Close to 14000km last summer, a trip to the XS650 Rally in the fall and all is well.  Had it out twice this month already.
Do any of you experience a phantom parasitic electric drain that will kill the battery in 3 days?  Additional equipment added by dealer are the Yamaha grip warmers, a fuse box to power the Denali LED driving lights, GPS and battery tender/vest outlet.  Dealer is scratching his head and calling in the Yamaha regional guy on this.   
Otherwise, no complaints that cannot be fixed with money.
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Welcome from another XS650 owner!  I'm in the process of selling my '79 XS650SF to help pay off the FJ.
Are you a member of xs650.com?  Just like this place, a great resource for those of us that like the old shakers.
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Welcome. I would look at the fuse box, GPS, and battery tender outlet. I assume the GPS is disconnected each shutdown? Try disconnecting the fuse box and see if the problem persists.
A government which robs Peter to pay Paul can always depend on the support of Paul.
George Bernard Shaw (1856-1950)
2015 FJ-09, Seat Concepts seat cover and foam, Cal Sci medium screen, rim stripes, factory heated grips, Cortech Dryver tank bag ring, Modified stock exhaust, FlashTune with Graves fuel map, Cree driving lights, Aux power socket.
2012 Street Triple type R (Wifes)
2007 FJR1300 (Sold!)
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!. I could not do without my regular access to XS650.com where my avatar is a black and white dog.
2. All the new wiring was done by the dealership so I am leaving it to be its puzzle right now while the bike is still under warranty. They had in it last summer and subjected it to tests including looking for a phantom drain and found nothing. The GPS comes off the bke when parked so all the obvious points have been covered off. It takes 2 or 3 days to run the battery down so if I am a daily rider, it is not a big deal. I will become more insistent with the dealer as my warranty anniversary approaches.
I plan to switch out the rear shock with a upmarket alternative and have already put on a bit bigger windshield, but it is still the Best Bike Ever. It reminds me of when I had a DRZ 400SM, but with twice the horsepower and an extra gear!
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Glad you are enjoying the bike.
I have GPS, OEM heated grips, Rigid Industries LED spot lights, McCruise Control, Warm & Safe Heated gear and touch wood don't have any issues.
As Ulewz said, check all the fuses and the connections (just cos the dealer installed your stuff, doesn't mean to say it is correct). 
Don't wait til the warranty is nearly up to get it fixed....it's not right and all that you have running shouldn't run the battery down in 2-3 days, in fact at all. The only reasonable explanation is something isn't turning off properly and is still drawing power.
Hope you find the issue.

Kimmie......the lady who likes to take little detours :)

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