Question edited for clarity.
Question moved to a Polaris Snowmobile category.
Rattling is almost certainly the automatic clutch. Backfiring could be due to a few things, and is often lean mixture via the carb rather than rich mixture in the exhaust.
Check the plug electrode. Black means it rich, chalky white means it's lean. The correct colour is a straw hue and no fouling. Backfiring is a well known issue. Check timing as well.
https://www.google.com/search?q=1994+polaris+indy+sport+440+backfires+through+carb
Rattling can be other things as well as listed here
https://www.google.com/search?q=1994+polaris+indy+sport+440+rattles
..
Remove the clutch cover then the spider (special tool required) there are some washers to add between the spider and engine side of clutch shaft to set pulley width. But before you do that when engine is off does belt have side clearance? If the answer is yes, you may only need a new clutch spring as they loose tension with time and idle speed may be engaging clutch
Certainly the carbs should be treated as a pair and so when one is suspected both should be checked. The cylinders will be unable to perform equally unless both carbs are tuned equally and synchronised at idle and at various throttle openings.
As part of the checking process it is important to ensure both cylinders are capable of performing equally. A compression test has limited use and a cylinder efficiency test is better. Injecting compressed air into the cylinder would prove the effectiveness of the valve seats and piston rings. A small amount of leakage of the inlet valve seat would make little difference to a compression test but it would make a great deal of difference to the way the cylinder performs.
Another important check is the valve clearances and also the ignition timing if it is adjustable. Some engines with twin ignition systems need to have the timing set for each cylinder.
? 6:05
https://www.youtube.com/watch?v=aEPx7OsywNk
Dec 11, 2009 - Uploaded by PolarisRich
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? 0:31
https://www.youtube.com/watch?v=oG2BWF4xVKg
Sep 28, 2011 - Uploaded by Trent Robinson
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