I have found highest RPM's can drop voltage a little. I believe because there is more electricity used for the spark because of more sparks per second.

Ah true true. i think he should be fine but if he wants to spend the monies feel free.

Adidasguy, so what is your voltage at 4000RPMs?
I understand that it may drop a little but I'm almost a full Volt away from where I should be. 

Jacob, I don't know why you say that I want to spend money. I never said that... I just want to fix the issue that is certainly present!
Every source, video, forum, manual I checked says that I should be getting 14.4 volts. I am getting 13.5V which is 0.9 V less. Where is that loss coming from is all I want to know and then fix.

Oh I'm just saying your going to have to spend money to replace stator haha, and i understand your frustration, believe me.

One thing to remember is voltage is measured with the battery charged.
Your battery, as I understand it, was not fully charged.

There is the usage of electricity verses the generation of it. Extra goes in the battery. When usage exceed generation, it comes out of the battery.

Until the battery is fully charged, voltage at the terminals can fluctuate.

Bad or smaller batteries will give different readings that a really good battery or one of higher aH.

I think you are OK. measure battery voltage after you ride. Then measure again in half an hour, then 12 hours later. Take various measurements. If a significant trend towards voltage drop when just sitting with the bike off, then battery is bad. a slight drop just after the bike is turned off may be seen. That's just some extra oomph from being charged and being warmer. It should/will drop off quickly. But after half an hour and from then on, it should be stable.

I think you're OK. No need to replace the stator. Your early tests showed it to be OK.

The second time I measured voltages today was after fully charging the battery with wall charger

Still think you're OK. Not the stator.

I recall that phenomenon when I've done some measurements in the past. 
Measurements I do now would not reflect your bike because I now have Shorai 14ah LiFe batteries and MosFet voltage regulators - sort of an improved electrical system.

As mentioned long ago, I have encountered bad regulators. Never had a bad stator yet.

I guess I will just leave it alone for now. But it would be nice to see 14.4V - it would give me peace of mind...
Thanks for all your help in pinpointing regulator as the main issue.

Those pesky regulator rectifiers... It would definitely be nice to have peace of mind, but as long as your battery is charged when you stop riding and not dying every time you ride you'll be a happy camper.