Can I get the results I am looking for with an ECM flash on the stock unit rather than a complete new ecm retrofit with a race tuner?
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It's not like the old days when the dealer could flash the ECM for what HD considered a Stage 1 modification, which usually consisted of a SE Air Filter and SE mufflers mounted on the stock headpipe. You could expect a reasonably close "tune" with that route. All that ended after the '06 model year. The PCIII was a good route to take back then, BUT there were a lot of so called "tuners" out there who used the PCIII that did not know WTF they were doing and you could get a tune that gave you 32 mpg. A GOOD tuner on the PCIII could give you a good tune and still get mileage in the low 40's at speeds of 65mph or less. 80mph? Mileage would drop down into the mid to high 30's.
To my knowledge, HD does not offer a "flash" for the ECM that would compensate for a change in headpipe, thus removal of the CAT...perhaps the Street Tuner would allow some changes, but all Street Tuner (as opposed to the Pro Race Tuner) calibrations would be EPA compliant (as mentioned). No cigar.
All you have to do to flash the ECM in the new bikes with a device like the TTS or SEPRT is have the "dongle" and cables, a laptop, pull off the left side cover, hook the cable up to the data port connector, and load the map. With the TTS and it's software, the FIRST step is to upload the Stock ECM map to your laptop's hard drive, a thumbdrive, a CD, or all three. Then load the new map. If you have a map provided by Fullsac for their setup, you're done. You can then fine tune the map either by doing some data runs yourself or find a competent tuner IF you feel the provided map is not good enough for you. The map I got from Fullsac with the header pipe, 2" cores, TTS, Cables was PLENTY good enough for my needs. You can even calibrate the inaccurate speedometer with the TTS software, if you want to. The bike ran fine and driveability was vastly improved. I did the work myself in my basement. Spent <$1100, and it took me about 5 hours, taking my time and having about 3 beers. If you have a decent socket set, some open end wrenches, a screwdriver or two, a Dremel tool or even a drill with a grinding bit, a laptop computer, and some basic mechanical/computer skills, it's a no brainer. Somebody who changes exhaust systems all the time, like a good shop, could probably do it in 2 hours or so. The bike appears bone stock but sounds and runs a LOT better. Loudness depends on what cores you get...the 1.75" are the quietest, the 2" are moderate, and the 2.25" are the loudest. But, even the 2.25" are not going to be obnoxiously loud. The 2" were fine for me, and I actually would have been fine with the 1.75"...but, I'm done with loud pipes for a number of reasons.
If you decide to go with the SEPRT, then you'll need to find a competent tuner to get it right...although there are probably a few members here who might be able to help you out with a base map...and that does NOT mean most HD dealer "techs". Some HD dealers have competent tuners, but they are the exception rather than the rule, IMO.