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you'll want to check the intake boots off the throttle bodies for cracks, if you see any cracks in the rubber boots then replace them asap. #1 cause blown motors as these boots were bad from the factory and cracked with in first year on most in 05. 06 boots were a better composit.
Also check compression on the motor to be sure its not losing any as it is about or past time in my opinion to refresh the top end. I would put the 06 pistons in it as the 05 stock pistons seemed to also have a bad batch and ended up cracking and alot of guys lost bottom ends when this happened. I would put 06 pistons in it before this season to refresh and prevent any mishaps.
as far as the clutch, get a used polaris clutch off ebay or snowest and throw it back on there. I think oem clutch is way better clutch then comet and with the right springs and helix you'll run spot on. theres alot of posts on here about clutching 900's depending on what you have for aftermarket performance as well. I have the 975 bb kit on mine so I don't know the exact springs for a stocker to tell you off hand. its out there though!
Drain chain case oil and get the chain case bracket update from the dealer for free. its an update and they will do it for free. had problem with chain case covers warping and leaking out all the chain case oil in these sleds as well. make sure you do this and get fresh klotz or other good brand oil back in it.
Buy side panel vents if you don't have them from someone like slp or 2 cool air vents like $150 a pair and put them on. this will give you the cooling you'll need to not blow belts every other ride. Also you want to get the slp torq stop arms for the motor which will be like $120 for both @ slp.com. these two things along with pulling some of the washers on the secondary bolt and putting it back on so it can move (float) some is the only way to make these 9's run reliable on the belt issue. for $270 or so you'll have the setup you'll need to not burn a belt but about once a season (1500 miles) for me. Figure belts are $160 for the good ones and $90 for the old style so it won't take long to add up vs. fixing the problem. had a friend who went through like 7 last year due to hot clutch, once he did just what I stated above it was 1 belt for the remainder 500 miles last year and its still on it in the garage.
If you buy a pipe buy the 06 slp setup and get the 06 flash done on the ecu as well. better mapping then the 05 setup.
if the radiator isn't gone junk it and get the relocation kit to re route it and block it off. it is worthless and about 25lbs of weight in the nose!
Slp slt or pp skis are a must too if you ride alot. stock skis suck and dart...
other then that hold on and ride it like its stolen, she will make you smile with that low end torq monster of a motor and if tuned and setup right it will be a great sled for you. otherwise if you ride it stock and don't do the few things above you'll hate it and be done with it mid season, i promise. wouldn't trade my 9 for anything except a turbo. nothing pulls it to this day thats non turbo of course its a bb 975 on 30 nos to
what clutch? Primary or secondary? Are you saying that the secondary is moving off of its axis around the jackshaft?
-Nolan