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Personally, I suggest you down the software from S&S, hook the ecm up to the computer and browse around. That's the starting point. Learn your way around the software, browse through the manual. Do the same for the software for the PCIII. You don't have to remove the PCIII to do any of that.
It can all seem daunting and intimidating until you actually do it. Most of anything we say can seem, pretty much, greek until you have a little familarity with the software and then things start making a little more sense. You can always come back and ask more questions.
If you zero out the map on the PCIII then effectively it's as though it isn't even there. So you don't really need to remove the PCIII. When you're done if you ain't using the PCIII for anything then you might as well take it off. Sell it on e-bay, give it to a friend, save it incase you change your mind. You could also just leave it on the bike. I wouldn't do that myself since there's a slight chance it might fail.
ok after pulling up the map on a laptop, wow. How do you know what the hell to change. All I see is different numbers. I'm not even sure what to add or subtract. On the PCIII there are to tabs on top. Fuel Table and Ignition Table. Is there a tutorial some were I can read before trying this. I tell you guy's this is intimidating..
I had the same problem with my 07 FLHTC and they replaced the O2 sensor and did a new download to change the timing and Voila! Runs better that when i got it new.
You loaded a new map on the PCIII or the ECM? If the ECM did you remove the PCIII? Whichever it was hopefully you saved the current map off it before loading a new map on.
Mostly I recommended you download the software and hook it up to the ecm to be sure you could. The easiest thing for you to do, now that you've seen you can, is order the knock suppression kit assuming it isn't already on the bike. Once you do that all you have to do is turn it on. It doesn't do anything you couldn't do, but it will automate what you would otherwise have to do. That's figure out at what rpm and throttle position it's occuring at and what's an appropriate adjustment.
Hopefully changing maps fixes it and you're satisfied with the map. If there's a noticable differance between the maps you can compare the maps. The PC fueling map is percentages by which to modify the injector pulse width. The fueling map on the ecu is pulse width. You modify it in basic mode by increasing or decreasing it by a percentage. So merging the fueling maps is straight forward though perhaps tedious. Most like all the PC map is doing is changing the fueling unless it's been dyno tuned.
Normally the fueling map is all you would play with. With timing you just don't have the information needed to set it. The exception is pinging since that tells you the timing is advanced too far. If there's a noticable differance in responsiveness of the engine between the two maps then that gives you an opportunity to understand what fueling changes do and what's a reasonable range for changes.
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