I have been reading until my eyes are about to pop out of my head.

I have an '06 Softail with the 141NU102-A0.MT6 download. Is there a new version of this canned tune? Does the A0 extension mean the version? So a A2, or B0 would be the update for the same setup with some changes?

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The latest files are available here for download: http://www.mastertune.net/files/calibrations.asp

The latest version of that calibration (#54)is 141NU102-B0. You'll need version 4.7.7 software to open it, though. You can get it at the sendspace.com website that's linked several places on this forum.

Does anyone know if this is a better tune, or an EPA adjustment?

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The easiest thing to do is download the latest Map and do a comparison of the two maps. You can open two Tuning Mode windows with a different map in each one and compare.

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2006 Road King FLHRI/Deep Cobalt
Stage 1/SERT
SE Pro Performance Exhaust

The first time you use the version 4.7.7 software to download to your ECM, the ECM operating system (not just the map)gets updated. Not sure what it does, butwhen I changed from v4.6.2 calibration 67to v4.7.7 calibration 67 there was a noticable improvement in the way the bike ran. There were some minor table differences in the new cal, but even after changing the tables in the new cal to match the old cal the improvement was still there.
An added feature is that with most of the closed loop calibrationsyou get separate closed loop bias tables to play with. I recommend you at least try v4.7.7 and the newest calibration. You can always go back if you don't like it...and yes, the ECM operating system gets changed back if you revert back to v4.6.2 or older.