Finally got back to this project, sorry for the delay.
You need to be able to first measure the position sensor's output when your cranking and when it finally starts, does the voltage change? 2.3Volts AC when cranking / will not start at all now, guess this is good at least it is hard failed.
Next, check the primary side of the coil, the procedure is in the manual as well, but you need a meter that can record the peak voltage since its not a constant output. Primary side 197ohms / there is battery voltage when key is on, drops down to 10.8 Volts DC when cranking. I think I maybe missing something with your description, peak voltage is just battery voltage here?
You need to see if the output from the CDI is changing when your cranking to when it finally catches and starts. What should this output be? I was clipped onto the two wires that go to the primary coil and just saw battery voltage when I was cranking, I am thinking I should see the voltage come and go so that the field collapses.
Although you said you have a new battery, I would have it load tested to verify, places like Autozone will do it for free. As a quick test, connect jumper cables from your quads battery to a vehicle battery BUT DO NOT START THE VEHICLE! Then try to start the quad. The increased cold crank amps will tell you if its the battery. Voltage min when cranking was 11.53. I did connect a battery with jumpers and did not see a change.
On a side not, check battery connections and such for corrosion. Since its an older machine, going over the connections and cleaning them and adding some dielectric grease would be a good idea, voltage could be dipping down due to resistance caused by corrosion. EFI machines are finicky when it comes to voltage. I have cleaned most of the connecters I could see with no flash cleaner and then applied ACF-50.
Thanks for your time!
Chad