I don't think that discards the battery. It might, if the bike was getting a full 12+ volts while being jumped. Earlier you said the injector had 10 volts. I know an X Bike will not run at that voltage. That low voltage could be due to being discharged, or it could be due to a bad cell. Also, 10V on the voltmeter isn't the same as 10V under load.
I don't know how the system is wired, but unlike most cars, the X Bike needs a healthy battery. If your battery has a bad cell, no charging will revive it and the bike will not run. So even if the stator is putting out 12+ volts, having the bad battery still messes with the efi system for some reason.
to eliminate this possibility, I would totally remove the battery and either replace it, throw in a known good battery, or wire it up to your car battery (without your battery in the system).