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Poor running Low Rider

This may be hard to remember but when you checked the spark at say a .040" gap with you tester, did you happen to see an orange glow around the spark or was the spark entirely blue in color.

You won't see any orange when pulling a spark with a wide gap. You will only see it when looking at the spark with normal gaps (~.035"-.050"). It is also kind of hard to see the orange when in sunlight.
 
An all blue spark is a weak spark. The orange barrel around a thick blue spark is what you want to see. That is a positive indication that your have good spark duration (burn tine) with reserve.

If you did (or do) see an orange glow or barrel around the secondary spark, AND the bike does pull good and hard in 5th gear without a miss or hesitation AND the spark plug wires ohm out OK,... for now I would say the secondary ignition is OK..

I work focus on the crank sensor having issues or the TPS having a flat spot in the wiper. You can't check the crank sensor with any reliability using just a meter. You just have to replace it and see what happens. But you can check the TPS with a good Fluke meter or continuity beeper.

I would also flush the IAC stepper just to get that possibility out of the way.
You may also want to test for intake air leaks with WD40 or propane.
 
My next step was to clean the iac, just didn't have any carb cleaner.
Shouldn't the tps or crank sensor set a code?
 
Shouldn't the tps or crank sensor set a code?

Regarding a crank sensor=> Yes, but the diagnostics will only throw a code when it detects a missing crank signal during cranking or starting. Once the engine is running, diags only sees a shorted or wide open sensor. Pickup output is RPM dependent, so slow engine speeds and cranking speeds are worse. Usually once the flywheel flags are moving fast past the sensor, a bad sensor looks "good". Also they are very temperature sensitive. As temp increases, sensitivity & output usually falls.
You have several symptoms which point to a possible crank sensor.

TPS=> Diags only pick off a really bad sensor which is either wide open or dead shorted. A flat spot can be missed by diags but it won't be missed or overlooked by engine mapping. Especially a fast recovering flat spot. If it only happens for say 100/ms, the diag are actually written to overlook it.
 
OK, I think I will run to the dealer in the morning and get a crank sensor see what happens.
Thanks for all of the help and ideas. Hopefully it fixes it.
 
They are not crazy expensive ($50) and if it does not help you with this problem, some day it will help you fix another. :)
 
Well, my crank sensor finally came in. I put it in and it didn't make much, if any differance. Cleaned the throttle body and checked for vac leaks. No leaks found. Checked all of the sensor connections, they were all ok. I rode it about 40 miles, still no codes. Looks like it may get a trip to the dealer this week. I sure hate to.
 
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