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Assuming he first started with a good base map... the auto tune will only auto tune if it's 'turned on' properly... ie; "turn switch on for 20 seconds turn switch off for 20 seconds" so on and so forth. Anytime the battery is disconnected, main fuse pulled, or total loss of power, this ritual needs to be performed upon re-powering up for the auto tune to take affect on the T-Max.
After I had installed my Rineharts I had bad decel popping. I was able to quiet it down some after finding and sealing a leak where the header pipe and muffle clamp together. But they still gurgle and pop little. Have come to accept it's just the nature of the beast because of the wide open nature of the Rinehart design.
Too rich, too lean, exhaust leak, and normal are the common answers, figuring out which one is correct is the trick. Personally I subscribe to the too rich and normal theories, once any exhaust leak is eliminated. You can't have a pop without fuel, air, and an ignition source, and you can't absolutely control fuel shut down on decel, always a little residual fuel from the on/off throttle transition. I don't care how rich you tune a bike in an attempt to cool it down, there will always be enough heat in the pipes to serve as an ignition source, so work the issue of removing air and fuel. I've tried all the tuning tricks recommended here and nothing so far completely eliminates it, I accept a little poping as normal, but thats just me. What I can say for sure is the richer I tuned, the more popping I got. Then again I'm just using a PCIII, one of those high end tuners may better mitigate the popping.
In most cases if it is not an exhaust leak the if your can richen the 0 throttle position it will go away. Not familiar with the Thundermax as I have PCV/AT good luck you will get it.
I resently had the same experience with bub true duels. retuned with the new feature the tts mastertune added which ajusts for cam base...ect didnt even use the data collection just the estamator function and all the popping is gone! like said before a leak in air,exhaust or retune.
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