I guess I would be concerned about the crank sprocket dot being missing to insure correct timing. Since you have been moving wiring around under the tank I would be concerned that something has been disturbed.
Are all fuses good? Fuses 1,2,3,4,6 and 7 should have power across them with just the battery connected. 5,8, and 9, I believe, receive power with the key on as well 10 for the park and tailight circuit. Other things to come under suspicion would be a faulty alarm if equipped, connector contacts, faulty neutral switch, clutch switch, sidestand switch. If you have fuel and spark along with adequate battery voltage it should be running. But you knew that....