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03 900 1m contant piston burn down

i have been struggling for 3 seasons with a burn down issue. up until now always mag side. I put 5 pistons in original motor, she finaly threw the rod threw the case and it was done. Installed a new used base with brand new top end. This motor ate 3 pistons. took the 01 800 motor out of my sons sled we were parting out. rebuilt, changing over, to a 900. got 300 miles out of this one and lost the clutch side this time, mag side looks bad too though, clutch side is a complete melt down, held it to the bar and fixed it good, bent the connecting rod too! the only common items that have not been changed are the computer, the oil pump, and the carbs. carbs have been completly gone through twice during this process though. does anybody have any bright ideas, other than junking it?
 
A bit more info to consider. We live in Maine and ride from about 500 to 3000 feet above sea level. The cdi box was changed when I purchased the sled from the dealer to a low altitude box. Jetting is very fat, at least 4 or 5 sizes above stock, mag side is one size over clutch side. Carbs have been gone through, and after the second burn down we discoverd that the high altitude needles were still in it, we changed tehse out to low altitude needles. I have a cdi out of an 01, 800 mountain cat. Would this work on my sled, I have checked and its not the same part number? Should I try it? I would appreciate any help any one can offer, this has gotten pretty expensive...
 
Does it run lean on the bottom? Is threre a low end bog or some other reaction like that? Are the pistons burning off the exhaust side at the top? If so then I would check the pilot jet remember if you have a low end bog it is from too lean of pilot jets and if it is from low end to mid range then start there. Also, you said you changed the needles did you also change the needle jets? Some times you can just change one or the other but rule of thumb is when you change one change both. From there even though you changed engines look for warped cylinders, check and see how true the bases are you might have an air leak which will drive you crazy trying to figure it out. Could also be the cases. To richen the mid range I'm sure you know this but raise the needles one or two grooves from center. Get a magnifying glass and make sure that the needles are right. Hope some of this helps. Just thought of something else,, it could be the ignition I know nothing about how to have it tested but I'm sure some one here can tell you.
 
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