My bike will not stat while starter motor is engaged. First start of the day can take up to an hour and need jumper leads to help the battery by that stage. Once started for the day it runs well and starts relatively easily, but only fires when the starter button is released.
I had the same problem. I placed a car battery in one of the side bags, it was only connected to the starter engine. Later I found out a much better solution; I replaced the yamaha battery to a gel battery with the same amperehours, it costed about 100 SEK more than an acid-lead battery, but was worth every "penny"
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All the Japanese bikes I have owned won't start in gear unless you pull in the clutch lever. There is a small plunger switch fixed to the clutch lever stock (the part that does not move). This switch is connected to the ignition and starter circuits, so when the clutch lever is closed the starter won't turn. Check the bike starts OK when not in gear. If you try to start the bike in gear and it does not start with the clutch lever pulled then the switch is not working. Hope this helps.
Sounds like your jack shaft isnt engaging into the bushing in your outer primary... you should pull off the outer primary and try carefully filing the edges off the bushing... Also check that the jack shaft has been properly installed.... This problem is common on customs
I would seriouly look at the starter clutch, the 1100 yamaha cruiser motors are notorious for this problem way back when the same motor was in the viragos and the xvs 1100 vstars, yamaha have tried to fix the prob over the years but stillhavn't got it right. if it just spins and whirs without engaging the engine, but sometime will kick in engagement, it sounds like your starter clutch is on it's way out. they cost from yamaha around $450- 500 ea plus around $350 to fit you have to include a $30 gasket in all that.