'03 Mountain Cat 900 Suspension set-up

I think you are trying to fix something that can't be fixed. I have an 04 900 and they just don't have trail manners. They are a mtn sled - not a trail sled. You will really notice it when riding with newer sleds that have better suspensions. They can take the rough trails better and usually ride faster so you have to ride faster to keep up - that's when the beatings begin.

If the shocks have never been done and it's an 03 then I would start there. Get those rebuilt, take it out on the trail and just keep changing spring rates until you find something that works better. Keep in mind, setting it up to have better trail manners might make it worse in deep snow. I would rather take it slower on the trail then give up any deep snow performance.

Level the front swing arm out. You may have to lower the rear if you do it. Keep the skid flat on the ground from front to rear. What happens is the track overtightens... so you run out of suspension as soon as the track gets tight. Stupid design on cats part.
Loosen your track up and push down on the rear bumper and look at the rear wheels....see how much they move rearward when the suspension compresses?...See the track tightening? Now over-tighten the track....push down on the bumper...Your travel is now next to nil...Theres your rough ride! This is also what makes the bearings on the drivers go bad. If you level that arm out, the skid won't move rearward as much and it will ride better. Its not a 100% fix but, it helps alot.

Revalve the rears shocks too. The factory valving left them hard on the top and then they gave up when they got compressed. Get them set up progressional, with them softer on top and get progressively firmer the more they are compressed. A lot of people set their springs on the highest setting trying to keep from bottoming out, when the culpret is the shock.