Just the fact that they told you that the problem was the regulator without testing the stator shows that their diagnostic procedures leave a lot to be desired. At best, it is very unprofessional, and makes them look like idiots.

I would be very suspicious that they only tested the DC output from the regulator instead of testing it properly. I would have asked them what tests they performed to determine that the regulator was bad, and I would ask them for the old regulator.

 

You're pretty close here actually. I went down to the shop today while they were putting the bike back together and I took a look at the old stator. It wasn't just bad, it was totally fried. It was shorted across a bunch of windings and had made a mess of the primary fluid. I'm a lineman and deal with similar stuff just on a bigger scale, and the fluid actually smelt like the oil in a transformer after a major fault. So the stator went bad, burned out some diodes in the regulator and, like you said, wouldn't charge much over 2000 rpm. Didn't seem to hurt anything else, and after a charge on the battery it test good with the proper cold cranking amps and maintained the right voltage. In the end, I didn't like how they went about it, but I'm convinced it needed the parts it got, and they cut me a pretty good break on the labor. I did make it clear that next time I better get a call from them before any parts get ordered or installed, instead of hearing from a buddy that was in that shop that day what all the problems with my bike are.
Thanks for the help anyways guys. Repair manual is on order, and hopefully other then a bit a help diagnosing, I'll be able to do most of the wrench turning myself.

 

Just to ease your mind some, that is exactly what happened to my 09 Heritage. The stator shorted and fried and then fried the diodes in the regulator. Luckily, for me the bike was still under warranty and didn't cost anything. So it can happen.