I'm having a similar issue but have already picked up some tips on this thread, thanks for posting! I'll share my progress as it comes.

 

Crossing my fingers that I got a bad CDI. I have a new CDI on order. I'll post results after it comes in.

 

As I feared the new CDI did not fix the problem. I have begun checking grounds again and all the wires in general looking for a problem.

Can anyone tell me if it is right that both leads to the coil ground out on the frame?

 

Update. Looking everything over I decided that the timing trigger pick up may have been out of adjustment on the new stator. Slowly moved it closer and after a few trys I am getting the LED on the fancy racing CDI to pulse. Still no spark but getting a little somewhere.

 

did u try putting new spark plug in ? ..or placing screw driver Into the spark plug cap and hold it close to the head while trying to start do u get spark ?

 

also did u check all wiering connectors ? if its new wiering so.e of the Wier's in the connector might not be connected correctly causing fault or not getting grounded

 

Something could be grounding like a safety switch or could easily be a broken wire in the stator. Have you tried to remove the kill switch wire on the CDI to eliminate kill switches? usually a black/white wire for a 5 pin CDI.
Also when you removed the remote/alarm box did you connect the pink and grey wires? (most are same colours) if not your kill switch wont work.

 

ATV Man funny you should mention the safety switch wires. I think I mentioned this in my original post but I was just coming back to ask about it again...

Every thing I have read says remove the black and whit wire (center pin on a 5 wire CDI) and you should be able to crank the motor and get spark, if indeed you have a faulty safety switch. The thing that has been bothering me as I chase this problem is that removing that wire changes nothing. I still have to have the handle bar kill switch on run AND either the handle bar or foot brake switch engaged to get it to crank with the safety wire removed. Everything tests right with a meter on the safety switch loop.

I have two different stators and I am getting 40 to 50 AC volts out of both now. I can get no reading of any kind out of multible CDI's. The "racing" CDI with the LED pulses with the pick up rotation. This leads me to believe I am missing something with the safety loop but for the life of me I can not figure out what. I have the plastics stripped right now because I had to do some frame welding. I removed all electronic components before I did this.

The remote shutoff is also bothering me but I get no difference with it hooked up or not. It only has 3 wires green, black and red and a green jumper connecting to a brown wire on the atv side of the plug.

I have done a quick continuity tests of any wire I feel is needed to get spark. I have checked connections. When I get time I will do a more thorough check but the safety wire deal makes me double think everything.
Any ideas? I feel I'm close and going to be kicking myself if/when I figure it out.

Edit/Update. I don't know if this means anything but earlier I asked if I should get continuity between the leads to the coil? Which I do. I just got to thinking that means the output from the CDI to the coil goes straight to ground. With all wires connected I get no output from the CDI. If I disconnect the ground lead (Green wire) on the coil I get voltage readings coming out of the CDI. Don't know if this means anything or not.

 

I get mid 40 volts AC from stator to the CDI. I get 15 volts out of the CDI to the coil ONLY IF THE COIL IS UNPLUGGED. I'm guessing the CDI is supposed to regulate the voltage to some degree and that is the cause for re-deduction. I have multiple CDI's and they all give the same readings. Can't decide if I have a coil problem or not I have 2 and they both do the same thing. Plug in the coil and voltage from the CDI is lost.

 

Have you tested resistance in the coil?