OPT, you hit it right on regarding the circuit breaker in the pouch. Pouch was full of rust and corrosion. So much for sealing in the pouch I guess.
I remounted it up under the front cover just under the pod and will make a cover for it. Can't be any worse off.
Haven't had time to warm it up as I've had company from Oregon but will let you know when I do. Probably next week as my wife is coming in tomorrow.
Thanks for all the help.

 

My 2004.5 had the same problem. (Intermittent Fan). I found the inside of pouch in same condition full of moisture and rust,circuit breaker terminals had to be replaced and mounted breaker up higher too. Perry

 

I don`t want to hijack the thread, im having the same thing with my 06 500efi,
the fan kicks in then it gets hot, stop for a second and the fan kicks on, i have looked for the relays under the light pod but i`m not seeing any no pouch nothing just the black box, put a new water sensor rad cap thermostat i`m lost.

 

You won't have the fuse block or circuit breaker on your model. You do have the control module under the front panel that has caused problems. It controls the fan operation and charging along with internal circuit breakers that can short out. If you haven't done so,eliminate the most common problems first. Make sure you have a good,fully charged battery,also make sure the radiator is clean front and rear,especially around the fan motor.Try to purge any trapped air by leaving the radiator cap off and topping off the coolant as the fan cycles on on off("IF" the fan does cycle properly) You can test the fan motor itself with 12 volts direct to see if the fan is the problem. Also the temp sensor on the left side of the cylinder can be checked with an ohm meter. At room temperature(around 68 degrees) resistance should show around 37.3 to 39.2 K ohms. At 212 degrees reading should be 2.1K ohms. If you've done all this and the fan "short cycles" and still gets hot,then it's probably the control module. Item #11 on this breakdown. Dirt Cheap Yamaha, Honda, Arctic Cat & Polaris OEM Parts & Accessories – Cycle Parts Warehouse
OPT

 

Finally got ou for a 50+ mile ride. Not very warm today but a lot of slow uphill downhill through heavy rock with no problem. After testing everything I'm pretty sure problem was circuitbreaker in sealed pouch.
Thanks to OPT for pointing it out.

 

Do u have a PDF of the 06 800 efi u could share I would appreciate it? Vikesfan1133@gmail.com thanks

 

Can't find a free one,but here's a cheap 5 buck pdf service manual.2006 Polaris Sportsman 800 EFI Service Manual PDF Download