Don't worry starting and running your scoot without CVT in/ on it.
This is usually done if you have any strange sound and you can't figure out where it comes from. In this case CVT off, motor started and investigate further.
For this starting issue:
Check again logically all parts you had removed.
-sparkplug itself
-sparkplug cap and cable until coil
-two cables on this coil
- killswitch again
- sidestand down or its switch, etc.
AND: since our injection scoots are a little bit picky when it comes to low voltage, check battery whether fully charged!
NOTHING can happen as long you keep your fingers off crankshaft.