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Im sure that couldn't have been a good thing for my valve train or crank right?
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If it happens only very infrequently, it is not to worry about.
1. Is the EITMS a comfort feature or an engine protection feature? I read this on the Harley-Davidson forum: This sounds a little like service rep lingo.
It is to protect the engine from overheating in stop-and-go. There is additional benefit for the rider and passenger, because if it gets really hot, it get also uncomfortable, right?
2. Are there any instructions how accelerate when the cylinder is cut off? I have yet to find any info in the owners manual on how to properly roll on the throttle when the rear cylinder is cut off. Its pretty touchy on my bike, and not knowing if its going to stall in traffic, is not part of the riding experience I signed up for. I think it can put the rider in a dangerous situation.
There is nothing else to do than accelerating. The situation you seem to describe should have less to do with EITMS having kicked in, but it sounds like the familiar hesitation many 110" CVO's do have. If you are using a tuning device (like the Super SERT or PC V), the hesitation can be removed. If you are not using such a device, the tech at your dealer may have a newer stock map to load into your bike EFI, which also heals the condition.
3. Turning it off- will doing so affect warranty?
I don't think so. Since you can turn it on and off by yourself.
Ride safely,
Louis