Battery slowly discharging with use, eventually not running cooling fan.  Have to use external battery charger frequently.
What needs to be replaced? Alternator, generator, stator?  

i would first check it with a meter and establish wether it is charging at all or not.
if it is charging even a little then most likely your problem is with the cdi box.
if it is not charging at all then well, polaris is well known for stators that go out fairly easily.