Hey, so what exactly is the problem you are having? Some details would be helpful so that someone an better answer any questions you have.
As far as what you already did ask, I would think that as long as it is spinning freely and not bumping into the stator or pickup coils you are good.
As far as I am aware, there really are no tests for the flywheel, its pretty much just a magnet used to induce an electrical current in the stator.
The item you would probably really want to test is the stator, and maybe you regulator/rectifier.
......I'd rather wake up in the middle of nowhere then in any city on earth.
*2014 VN900 Custom (16,200 miles and counting)