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I just had this conversation with my mechanic. He claims if you know what you're doing or follow the training video worth a damn, the SERT is the better way to go. He claims that the TM with autotune is too "safe" of a tune for him and there is little you can't do with the SE that the TM can. Neither is really cheap but the SE unit with all of the cables, connectors and training video is still not as big of a nut as the TM box with Autotune.
FWIW, I will be getting the SERT.
That said, unless you plan on making a lot of changes, there isn't much use in getting either. A Fuel pak or PC3 will do great and save some coin for more chrome.
I went with the TTS Master Tune and a custom dyno tune. With the TTS you can change the ignition timing tables to prevent detonation. My goal was to get the best performance in the low and mid ranges.
Before the tune I never used 6th gear until 60-65 mph. After the tune the bike slips into 6th at 50 mph and pulls harder in 6th than it did before in 5th.
Thanks for the info. I plan on making some modifications... cams, pipes new heads... will probably go with the 113ci SE Race Kit. The mechanic at my local Harley dealership said I should go with the SE tuner; one of the local custom builders is the one who suggested the TM tuner. I think ether way I will happy with the performance it just comes down to dependability. I will also look into the TTS
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