Was talking to an HD rep and he told me the EITMS was only there for rider/passenger comfort.
I dont know if I believe this.
I have thought about turning mine off, but keep thinking it has got to be better for the engine to leave it on.
I have done all the mods, same as most here, tuner, exhaust, etc. but I do a small amount of in town riding and am sick of the one cylinder idle.
And yet like most here want to do what is best for the life of the engine.
Harley has stated all along that the latest EITMS was for rider comfort, but you are wise to only partially believe it. Certainly it was a response to all the complaints about heat broiling riders legs and private parts, but I also believe it was a response to all the rear cylinder mechanical failures they experienced in '07. If you consider that the cylinders, head gaskets, etc. are the same for both cylinders, why were the failures almost exclusively on the rear cylinder? Heat is the simple answer, the rear cylinder runs hotter than the front under all conditions, but especially when running at low speeds and at idle.
The earlier models, such as my 2005, had a simpler system that just varied idle speed, ignition timing, and eventually air-fuel ratio. Eventually they could reach the point of what was called "skip fire", where the rear cylinder didn't fire on every power stroke, but they didn't actually shut down the cylinder completely like what you have now. The big difference with the system introduced in 2007 was the actual shut down of the rear cylinder, and the significantly lower temperature where the system kicks in. If you look at the attachment, you'll see that the skip fire feature didn't kick in until the front head temperature reached 356°F on the '02-'05 models, then in '06 Harley dropped that temp to 329°F, and now the '07 and later bikes shut down the rear cylinder at approximately 287°F. So current models with the system enabled are much more likely to have the system kick in, and when they do it's much more obvious since the cylinder isn't firing at all.
If it were mine, I'd leave the EITMS system enabled, but I'd also make sure I had tuned the bike to idle at a richer (cooler) AFR and reset the closed loop AFR's to a richer and cooler figure as well. You might want to verify your tune if you are having the EITMS kick in too often; many folks who've gotten a custom tune have indicated they rarely have the EITMS engage.
Jerry