You definitely have some burnt wiring! You need to trace back into the sheathing to where the wires are good and splice back into them. Looks like this small module taped to the sheathing at the front is a resistor module,but the connectors don't look factory?Does show on the parts breakdown this is replaceable on the harness. You also do have the black finned Chinese ecm module. Looks like the choice is yours on this one, either to tear into the wiring harness and try to patch it up or just replace it. BUT even you do replace the harness you could still have a burnt up cdi or damaged ecm module also! Harness is about $225 at Cycle Parts Warehouse including the resistor module. Look here at the harness and at item #9 (resistor module).Dirt Cheap Yamaha, Honda, Arctic Cat & Polaris OEM Parts & Accessories – Cycle Parts Warehouse If you'd take it to most shops they'd replace the harness as the labor would eat up the cost of a new one in tracing down wires. Just depends on how much time and patience you have in doing this!
OPT

 

OPT, Should I start with re-splicing the wires that are melted and get a new battery hooked up properly and see what happens? What do you reccommend? I hear those resistors can get hot but still work. all connections to the resistor were good, no melting. Outside of a winch and handwarmers installed by the dealer I have not other things done to this atv. I think I will start by replacing the wires tonight, any idea what gauge that is off hand so i can pick it up on the way home?

 

Just take a piece of wiring down to your local auto store to match it up. Most wiring was 20-22 gauge if I remember correctly.Resistors do run warm. Hopefully it's not as damaged as much as you have feared. Could be just a few wires up in the main sheathing that is the problem. Worth a shot at repairing,plus use some good shrink wrap connectors that can seal out moisture. Good luck and keep us posted. OPT

 

None of the wires are actually damaged I wiped the melted sludge off them but wires were still good?

 

This melted sludge came from somewhere? You still might check up further into the harness and check for any wires that could have melted and dripped onto the ground wires.Plus check for any soft wires that may have have burnt up internally. OPT

 

I put In a new ECM and its fixed! Thanks for the help

 

How does a 2004.5 miss the recall when the recall has a 2004 ,2005 and 2006 on the list? ATV:Spam word Polaris Ind. expands recall of ATVs

Is it like they had it wrong in 2004 but corected in 2004.5 then got it wrong once again in 2005 and 2006?

 

I ran my vin online and with the dealer I have the 400 and my model wasn't recalled. It's fixed for under 150 and the place that sold me the wrong battery is covering the cost if the ECM!

 

I ran into the same problem on faulty ecms not on the recall list,but Polaris ended up covering them when I called either of the two Polaris engineers I dealt with the most. The main recall was really just a generalized round up of the year models most affected and the engineer I talked to knew other models would be affected not in this list!! This was a nightmare then in 2005 when i first started replacing ecms and seems it's gonna last for a long time! Glad you have the problem solved. OPT