Welcome, Adam !!!
Something in the circuits must be open or not working properly.
I assume the transmission is in Neutral.
http://faq.ninja250.org/wiki/Underst...afety_switches
http://faq.ninja250.org/images/0/07/..._Schematic.pdf
If you are able to produce manual sparks, the problem is not in the source of power or circuit or the coils or plugs.
Either the electronic box is bad or grounded via a safety switch, or not feeling any signal from the pick up coil or the box-coil circuit is open.