IMO... for peace of mind... I'd replace the pistons.... if one lets go on the 900's you will usually damage more than just the cylinder...
2000 miles on the 2006 900's is a good mark for a refresh... at 4000 I'd re-nic/hone the cyls for pistons.
On a 2005... I'd replace the pistons with the new style in the 06... the 2005 design is not even made any more... The SPI pistons are not a viable option either as they are a copy of the weak 2005 pistons. Wiesco pistons are forged and have more concerns for the everyday rider than cast.
Go with stock Polaris (Elko-Austria) pistons when you rebuild it.
I have seen many untouched 06 900's go 4000 miles without issues... It's not a competion to see who can get the most hours out of your motor but getting good compression and reliable power from it.
Do a leakdown test and compression test on the engine, ...pull the Y-pipe and check for wear patterns on the pistons and cylinders...
5000 miles of hard trail riding, IMO, would equal about 1000 miles of HARD deep snow use... One persons riding area, snow, agressiveness, intake, dirt etc will not match anothers.... no will the wear-n-tear on the engine and its internal components.
At this mileage... check your crank runout, pull the primary and have the balanced and checked (I like Indy Specialties work for how thorough they are)... check for cracking on your throttle body boots and the motor mounts...
If you do the top end... take the little extra time to pull the whole motor and do it on the bench... you can do a better/cleaner job there and it gives you a chance to check the steering gear and clean the filthy oil-soaked bulkhead as well as the very important motor mounts. Those issues are as important as the pistons themselves.