Does it matter how you connect the wires on the Stator

No it does not matter. That is why they all have the same color.
If you check for resistance with an Ohm meter between either one of the yellow wires and the chassis there should not be any (infinite resistance means stator is OK).
Measure the output voltage between each pair of the yellow wires (3 measurements). At idle you should get 12-15V and at 5000rpm more than 40V on each pair.
If all the above stand correct you probably need a new regulator/rectifier assy.

The yellow wires can go in any order (its does not matter as long as the wires are one yellow wire to one yellow wire. They melted most likely because the connector was corroded (had a bad connection) or the charging system has an issue. Put a new connector on it. Run the engine @ about 2500rpm for about 5 minutes, then grab the connector with your hand to see if it is hot to your touch. If the connector is not hot then most likely the charging system is ok and if the connector is hot, then the charging system has something else wrong in it.

Locate the wire harness coming out of the stator on the left crank case cover of the motor and follow it to the plug with three yellow wires. This is the stator plug. You should have continuity between any combination of the three yellow wires, but no continuity between any of the yellow wires and ground. If the stator yellow wires are grounding you will have to replace the stator. To replace the stator remove the left crank case cover and unbolt the stator from the inside of the cover. Do not forget to purchase a new left cover gasket with the new stator or you will just delay your riding.

Locate the wire harness coming out of the back of the motor and follow it to the plug with three yellow wires. This is the stator plug. You should have continuity between any combination of the three yellow wires, but no continuity between any of the yellow wires and ground. If the stator yellow wires are grounding you will have to replace the stator. To replace the stator you have to remove the motor from the frame or at least unbolt the motor and rotate it enough to remove the rear cover and unbolt the stator.

polaris factory stator (not starter, STATOR) are junk and are prone to failure. The coil can be checked by checking the resistance with an ohm meter. To check the stator, follow the wire harness coming out of the engine by the recoil rope. Follow them to where they connect to the CDI, coil, and rectifier (should be around the headlight area, under the plastic. Remove the pair of three wires in one connector (should be a green, a red, and a red/black). Check for ohms between each. If any show open, the stator is gone. To replace, you have to remove the recoil cover, flywheel, then the stator coil comes out with four screws.

Hi the three yellow are all the same, they are the alternator wires, are connected to a common star point, so will not matter as long as they are going to the 3 yellow on the other side of the plug.
As a quick test of the stator, any pair of these yellow should produce the same resistance, none of them should have continuity to ground, and any pair with the engine running should produce similar AC voltage, maybe 40-50v

Best bet is to take the rectifier back to where you brought it with the old one and ask if they are compatable .connecting up the wrong wires could damage the new unit .

i dosent matter just connect the yellow wires to the other yellow wires it will work fine

Hi and welcome to FixYa,

Almost always, your described problem could either be a defective rectifier/regulator combo (most likely) or loose, burned or corroded connectors of the 3 yellow wires from the stator to the regulator (likely) or burned/open stator windings (least likely).

You would need a multitester to verify which is faulty by considering:

• at idle, output of regulator should be around 12.5 volts and go up as the RPM is increased to about 14.5 max;
  
• the regulator's output is directly connected to the battery's + terminal;
  
• the stator uses 3 coils connected by 3 yellow wires to the regulator. Due to high charging currents, these connectors often gets burned and loose conductivity/connection. Check for burned terminals/connectors or discolored plastic tab;
  
• the stator could be checked for continuity. Each yellow wire should measure 0.3 ~ 0.5 ohms to the next yellow wire at any yellow to yellow pairing;
  
• in most instances, the yellow wires should not read a connection to ground with the connector to the regulator removed.
  

Good luck and thank you for using FixYa.