Sorry you are having trouble. If your in the twin cities area Minnesota I'd be glad to stop by and help.
No spark..... Not sure what this simple harness diagram you were given looks like so not sure where to start.
To expand on jetblack's igniter wire breakdown:
Yellow&Red: Plugs (Positive supply) I run a key switch and the "run" switch on the RH controls. So key switch sends power to RH switch. RH switch sends power to coils and igniter. If you are just going to have toggle switch then run power from toggle switch to this wire and to the coils positive terminal. Remember if your throttle stick open while riding you'll have to try and turn off you toggle switch to kill bike.
Green: Plugs (left coil)
Black: Plugs (right coil)
Black&Yellow: Lights & Negative Battery post (Ground)
Yellow: Pickup Coil (leave wired as is with 4 pin wire connector is easiest)
Red&Black turns into Black: Pickup Coil (leave wired as is with 4 pin wire connector is easiest)
Blue: Pickup Coil (leave wired as is with 4 pin wire connector is easiest)
Black&White: Pickup Coil (leave wired as is with 4 pin wire connector is easiest)
Brown&White: Diodes (ground or ground through safety switches)
As far as the safety switches. One wire from the ignition module (brown/white stripe) that gets split into three wires and goes into the Diode. Three wires come out of the diode and one went to each safety switch (I don't remember colors and on-line copy is very hard to read) The ignition module is using this brown/white wire to look for a ground to say it is OK to have spark.
SO
If you have removed all three safety then just ground any one or all of the wires exiting the diode. Or remove diode and ground the Brown/white wire from the ignition module. Now Ignition module should think its safe and give you spark. (The diode is there to stop flow of electricity back into ignition module due to the way the safety switches are wired)
The system is set up so all three safety switches need to work together so bike will stay running. So it doesn't really work when just eliminating one safety switch. If this is the way you want to go write back what switches you want and I'll walk you through if it can work and what to do.
Now if safety switches are bypassed and still no spark.... Then maybe look at if the coils are wired correctly. Yellow/red are positive. And I believe Green is left coil and Black is right. (correct me if I'm wrong guys) If you have the green and black switched you should still have spark but bike won't run due to firing in wrong order.
Good luck.
Brian