02 suzuki eiger 400. couple of the magnets came off rotor. chewed up the magnets and wiring on stator a little bit. cleaned up best I could and put back together. runs fine but wont charge. is this because of the magnets missing or could it be the stator wiring? not sure how it all works so was wondering if i could replace stator and be ok . rotor is expensive and special tools to take off. not sure its worth the cost.

SOURCE: not charging, removed the regulator, has three

(I am the author of the reference thread on TriumphRat that wasposted by another respondent)

Not personally intimate with the Vulcan, but this is a 'conventional' motorcycle 3 phase stator energized by a crank driven magnetic rotor. 
The stator is connected in delta to the R/R. There should be NO measurable resistance from any of the three stator output terminals to engine ground - it should be completely isolated.   If you can measure a low resistance (not clear if your 0.2 ohms is from terminal to terminal or terminal to engine ground) then your stator is fried. 
Regarding the R/R connections - the third wire on the output is one of two functions (unfortunately without benefit of a schematic I cannot definitively conclude for you): either a 'voltage sense' wire, or in some Kawasakis they feed one phase of the stator output back out again for use in the starter cut/latch circuit. It should be reasonably easy to differentiate which it is. 
Good Luck! 

SOURCE: 400 Eiger ATV, starts and runs fine, stalls the

If 2 stroke check crank seals, check plug cap for proper resistance,check for good fuel flow to carb.Spark should jump at least a 1/4" gap,NOT JUST the .030 or plug gap.

SOURCE: suzuki eiger 400 is overheating

sounds like your thermal switch that controls the fan isnt working, that would be the first place to look, try connecting the two terminals to the thermistor and see if the fan comes on, good luck