Are you running on original pipes or have you installed aftermarket pipes that are louder ?? I had the same problem with aftermarket pipes and come to find out my carbs were not jetted the way they were supposed to have been done when I installed the pipes.Also there are two chrome tubes starting at the front of the engine going under the seat towards the rear--- there is a rubber hose connection connecting each side .You should disconnect these hoses and bypass the tubes-- in other words use one hose to connect the front two tubes together and the other to connect the rear tubes together , its some sort of early emmission thing that will cause some backfire
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The primary cause for backfiring on deceleration is an air leak - if the baffles have been removed or modified or if the gaskets in the exhaust tract are not sealing properly, fresh air can be introduced into the exhaust stream causing a pop or backfire. Check your exhaust system - especially if you have recently had an oil change, since the pipe has to be removed to change the oil filter on this model.
is it a straight thru exhaust, or is it just a head pipe with nothing attached? If it's just a head pipe, you need to get some sort of muffler on it or you'll burn your valves out from a lean condition. The backfire is due to the vaccum fed carbs that yamaha runs. They work wonderfully, but under heavy deceleration, the vaccum still feeds the bowl, and it builds up excess fuel, which eventually burns off as a backfire. If it were fuel injected, you could have the fuel map adjusted to lean it out under deceleration.
It sounds to me that your carbs might be a little gunked up - you mentioned the gas may have been old, so it's possible that the smaller (idle) jets are slightly plugged up. Fresh fuel might do the trick and/or you could try using a fuel system cleaner and water remover. This problem might 'solve itself' with a little time.
As far as the backfire - this might be either from the carb issue or it could be related to that rattle you mentioned - you could have a loose connection at or near the head - this can **** air and cause a backfire.
Does the bike backfire only when the throttle is being closed? The carbs have a idle enrichment circuit. If the idle enrichment diaphragms are stuck in the closed position, the bike will backfire when the throttle is shut down. You can't remove these parts for cleaning without seperating the two carb bodies (and then needing to synchronize the carbs after reassembly). A trick that worked for me...fresh fuel, and some fuel system cleaner in the tank...ride the bike at highway speeds for 20 -30 minutes...repetedly rev the engine to a high RPM then shut the throttle closed. The repeted application of high engine vaccum to the enrichment diaphragms freed the stuck diaphragms and the fresh fuel cleaned any gum and varnish that caused the trouble. I've put 20,000 miles on it since then with no backfiring.
I am not sure what you mean on the "running fast" statement. If idle speed then turn the idle screw outward to slow down the idle.
The backfire is caused by turning off the ignition key when the bike is at high revs. let it idle down THEN turn it off. The backfire is there because the carb idle circuit is active anytime the piston is in motion. Gas goes into the cylinder as the bike revs down then a hot spot in the exhaust pipe finally ignites the built up gas. There is your backfire.
Is the running fast question answered? Give me more information on the problem if it isn't.
With the key off and the engine "running down", the idle circuit fuel is still going to into each cylinder then out the exhaust. A hot spot in the exhaust can ignite the unburned fuel creating an explosion, ( backfire ). Let the engine run down to an idle THEN turn the key off.