Do you have your instrument panel setup ? Do you see the neutral indicator "on" ? If the neutral switch isn't activated, the starter relay won't activate - UNLESS- you pull in the clutch lever instead to start the bike. So, either clutch switch must be installed and active (it grounds a pin on the starter relay (can't recall which one at this instant) when active... or the neutral switch ahs to be grounded - which would indicate gearbox is in neutral ordinarily, but if you've got the gearbox disconnected or you are SURE it is in neutral you could "jumper" the 2 neutral switch wires.
Maybe check the wiring to see that these switches are both wired up correctly and the neutral light is happy?