I have a 2006 C90T and had the exact same issues. I have no great solution for you other than to tell you that in my case it turned out to by the stator. This is one of the only known reliability issues with this bike. With the regulator and stator setup on the standard C90 the stator is basically 'running' all the time due to the type of regulator/rectifier. What myself and many other have done is to replcae the regulator with Cycle Electric CE602 (made for Dynaglide Harley). This type reduces the load to the stator hopefully extending the life of the stator. The CE602 is much larger than the stock one and will have to be relocated. All my power issue went away once upgrading to a better charging system. To be sure though I would get it into a shop to have them test it right.
Regards,
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