Ordered a new harness and everything lines up but these extra wires coming out of the engine next to the stater wires. There is also some kind of switch coming out of the rear of

extra plug that come out of the engine next to the stater

switch that was mounted to the rear of the Quad

same wiring coming out of the engine next to the stater
the qaud. Do I need these wires hooked up and what are they for.

 

the middle picture is a tether/break away switch

 

Usually you get stator wires for battery power, trigger coil wires to CDI and exciter coil wires to CDI coming out of stator housing. If you have all these accounted for, there could also be gearchange light/indicator wires, these would not be needed unless the neutral indicator wire also goes to the starter solenoid, so it can only be started in neutral. Probably pale green/red, check if it goes to the solenoid.