This just happened to me on my '03 TRX350FM yesterday. I started smelling something electrical getting hot and all of the sudden everything died. Check the fuse panel and the main 30 amp fuse had blown. I replaced the fuse and it started right up, moved about 3 ft and the new fuse blew.
I started searching for a short with my Fluke meter, but when I got back to the rectifier I could smell that it was burned.
Pulled the plug on the rectifier and put another fuse in it, fired right up and ran perfect.
I ordered a new rectifier, but I'm a little worried that something else may have caused the original one to burn. I guess it could have been overworked from the previous owner that had some sort of winch on the front. I've just learned from the A/C tech business that changing parts blindly can end up being costly, I always prefer to trouble shoot and diagnose what caused the failure.....especially with a $70 part.
I ohmed out the three yellow wires from the alternator/stator (at the rectifier plug) and they ohmed out fine, also checked them to make sure they hadn't gone to ground. I started it and the output voltage was around 18vac on all three yellow wires at the rectifier plug (between each leg to ground). The only thing that worries me a little is that I've read that the AC voltage from the alternator should be in the 30vac range?
Anyone know what voltage range I should be seeing from the three yellow wires off the alternator windings at the rectifier plug?
*EDIT - I went ahead and plugged the new rectifier in and all is good.