You say you have the manual - if it is the service manual all the electrical troubleshooting and wiring diagrams are in chapter 7 - page 7-21 in particular. There are some safety interlock circuits involving the clutch, side stand, neutral position sensor in the transmission, "run/kill" handlebar switch and ignition switch that all need to be working properly (or correctly bypassed) in order to both allow the starter motor to run and ignition to fire.
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