Ignition cuts out when put in gear even though side stand switch has been bypassed

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Is that tuneup information Gen I?

There are some differences in diagnostics displays and things like segments in the display vs temperature.

Not sure if suspension settings and specifications are identical between generations either.

Gen III+ is, of course, another beast entirely with respect to displays and spark plugs. And ES suspension.
Not everything is the same but there are useful bits (fault codes as one) that are good across the board.

Use your Google Fu if concerned. I did just now and came up with this link ez pz.

https://www.manualslib.com/manual/802254/Yamaha-Fjr1300-S.html?page=23

 
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I've also had the switch on the clutch lever fail (keeps the bike from starting unless it's in neutral or the clutch lever is pulled in). Easy to jump & see if that solves it as well.

 
Update to my issue. So I cleaned up the wiring properly; exposed fresh wiring and soldered the bypassed sidestand switch wires and waterproofed them with shrink tubing. I've put on 10 hours of riding and not a hiccup, so all is good. Oh wait, today while riding in rush hour traffic so happy that I'm finally starting to feel that I can trust the old girl again, I notice that my turn signal indicators don't light up when I'm using them. Then the check engine light comes on when I'm parking it at work. I run diagnostics and there is no error code whatsoever.... dammit! And there goes the trust again.....

 
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