By "stock setup secondary" do you mean the stock helix?
That was a major problem with these sleds.
Hmmm..
The clutching has been pretty much worked out on theses sleds by trial and error.
Motor mounts, belt life and a lot of other concerns are things that will benefit from changing out the clutching/gearing
What I'm reading you have
Primary weights Polaris 10-68
Primary Spring SLP Blue/Pink 140/360 (actual when compared to Polaris measurements)
Secondary Spring Black/Red 140/240
Secondary Helix 64/38-.36
Gearing 19-39 2.05:1
You did not indicate the belt that you were using, but I would ONLY recommend 3211115 from Polaris as there are no aftermarket belts that come up to the std of this belt from Mitsuboshi (not misubishi).
One of the most common setups for your sled at your altitude would be
Primary spring Polaris Almond (AKA Black-3342 pn 7043342)
Primary weights for your altitude 10-68
Secondary helix 66-44/42 run in the 44 position.
Secondary Spring Red/pink 140-260 (The stock red black 140-240 will work ok for some too)
Change out the gearing to 19-42 and make sure you use good quality chaincase oil and that the chain has proper tension.
Make sure that the belt, pn 321115 has been washed with super hot water, scrub with a stiff brush on both sides (do a good job), rinse well with hot water and hang to dry.
Now... here is a detail not to be taken lightly... The belt side-clearance from the factory was not set for the width of the 3211115 belt. This must be reset and most people don't have the tools to do this with. I suggest that you send in the clutch for re-balance and clean up... this is THE primary connection from your motor to the sled make sure it is as spot-on as possible.
Once installed, the belt deflection can be set easily, take your time to do it correctly. (in your Owners manual)
New springs every season.
If you have a high mile clutch... Definately have it serviced.
The clutching system is the heart of your sled and its performance...This is the one area NOT to cut costs on.
Also, most 2005 900's that I've worked on have broken motor mounts that also affect the performance...unfortunately, you cant service these or even check them without pulling the motor...