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Intermittent Miss

this morning it ran so bad for a mile that I almost headed back home.

Since it was running very bad for about a minute, you may want to perform a another WOW test just in case diagnosics happen to grab a code. When it was running bad for that mile or so, did you happen to notice if giving it more throttle would make it run better. Or was more throttle just "more worse".

Definently check for codes once again.
 
TQ's post #17 reminded me that I have read about bad injector connectors, or broken wires nearby. Those are worth checking, and wiggling as suggested. I am less inclined than before about it being a dirty fuel filter, they usually flow or don't flow. When it runs badly have you noticed any electronic malfunctions? Like speedo or tach needles bouncing, signal lights flashing?
 
TQ's post #17 reminded me that I have read about bad injector connectors, or broken wires nearby. Those are worth checking, and wiggling as suggested. I am less inclined than before about it being a dirty fuel filter, they usually flow or don't flow. When it runs badly have you noticed any electronic malfunctions? Like speedo or tach needles bouncing, signal lights flashing?

Harley Davidson Forums I wonder what the date of manufacture of the engine and injectors are? Injector error codes - Harley Davidson Forums - HDTimeline.com here is some more reading on the injectors
 
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Checked for codes as soon as I got home. No codes set. I did not try whacking the throttle wide open, but I was accelerating away from a stop when it started acting up. I continued to accelerate and there was no change in the way it ran. It continued to cough and choke until the end of the mile where I have to turn. When I left that corner it coughed one time and ran perfectly the rest of the way to work. Through this whole thing I have never seen the check engine light come on, nor have I observed any gauges bouncing or lights flickering.
 
There is something I don't understand here, well lots of things I don't understand, but how can it run that badly and never cause the check engine light to come on?
 
Harley Davidson Forums Do you know if this has been gone to your ECM?

Jack, I'm not sure what you wanted me to see here. Your link took me to another post about an ECM program change that contained another link to something else. I could not open the second link so I'm not really sure what this involved. I had the ETMS turned on and a stage one download done in the fall of 2010. I assume that would have installed the latest upgrades. Does that answer your question?
 
There is something I don't understand here, how can it run that badly and never cause the check engine light to come on?

In most cases, an extreme set of conditions need to be met for a DTC code to set. Examples are: a DTC code for a missing crank sensor signal is only set while cranking the engine for a time that is longer than 10 seconds. A DTC for the engine temp sensor is only set when the sensor measures near wide open (infinity) or dead shorted (near zero ohms). If the sensor is fixed at one value, a code won't be set. And there also are no DTC's for low or high fuel pump pressure as Tank already has pointed out..

Yes, it's better than having no built in diagnostics at all, but it's also not much help in a lot of cases. If a professional tech needs a code to fix a problem, he won't be fixing many hard to find problems.

Before digging into this problem, are you comfortable reading schematics and using a meter. If it's a problem that isn't common and takes some time with trial & error, would you rather take it to a shop and pay someone else to figure it out.
 
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