Not sure about how the 06's are set up? I purchased an 05 this summer from a guy that seized it up. This is my first experience working on a ski doo. Being an industrial line mechanic, I guess I have a thing for projects.
I took the motor apart, (2078 miles on it) found that the mag side was the worst. The pto side was getting there. I pulled the motor, relocated the low pressure fuel pump by the battery, checked the crank for play, did not notice anything wrong with it but it ended up costing me as I am currently looking to rebuild the crank due to finshing up the top end rebuild and taking it for a test drive. It ran strong for 15 miles as I was breaking it in (nothing over half throttle) Then it just died on me. I took it home after noticing the motor was seized again. I pulled it apart and found that my lower connecting rod bearing on the mag side exploded and shot fragments of the cage into my cylinder and out my expansion chamber. I have to buy another piston/rings and replace the crank. Luckly, the replated cylinders didn't get beat up!
Back to your questions. I don't know if the 06 air box is the same as the 05. If it is, get rid of it and get some pods put on. These big motors injest the belt dust from the poorly sealed air boxes and when this happens, you get a sled like the one I bought, The reeds were clogged with belt debre which tells me the motor seized the first time due to debre in the cyliner and eventually it took out my lower connecting rod bearing.
If you do go with the sled, and the above mod has not been done, you would be wise to clean the reed cages out and throttle body and put some pod filters on it. If you find alot of debre in the reeds, you better dig deeper into the motor and do some preventive maintenance so that it doesn't leave you stranded in the back country. The power is unreal and addicting. I can't wait to get mine running again.