I went ahead and ordered a Yamaha Bruin service manual. If all else fails i'll rewire everything how yamaha did theirs and just hope the 4x4 and lights work.
I think the cdi has a fault of some sort since the spark plug is getting constant spark without the flywheel spinning and without the start button being pressed.
I'm going to take apart the starter motor and clean up the contacts and hope that fixes its anemic attempt at turning over the engine. if not i'll get a new one. I feel like i'm close to getting this running, i just need to fight the wires.

 

Fairly sure the Bruin is AC CDI if you are getting a constant spark, either your bike is DC CDI and something has gone wrong with it or, if it is AC, power from the battery is being fed into the CDI when it shouldn't be.

 

I haven't been able to tell what kind of CDI it is. Its fairly large which most sources say is indicative of a DC. I'm going to split the harness open and see whats going on inside.

I think the problem with the starter is somewhere between the bike and pavement on a good day. I've been using a 6amp charger which may not be enough amps by itself to feed the motor to turn the engine. The battery is long dead and gives less than a volt on a meter, i should probably get a good one to continue working on it.