Aaron - let's try again.. All those coils in the stator are wired in series like a bunch of Christmas tree lights. With both ends disconnected, there should be no continuity to the engine block - check that by touching one meter probe to one of the two stator wires (with BOTH disconnected) and touching the other probe to a clean spot on the block. If you show continuity, the stator coils have a short to the block.
To check to see if there is an open coil, touch a probe to each of the stator wires - you should measure a low resistance, but you need a multimeter with a low ohms scale, like a maximum 20 ohms range, to accurately check that. IF you can see some continuity, and if the check for a short to the block is negative, the stator is probably OK...
Testing parts of the circuit with some things connected and others not usually doesn't result in a meaningful test.
This isn't really a complicated charging circuit, the stator and flywheel generate simple single phase alternating current, the regulator pack changes it to direct current and clamps it down to the 13 volt charge output..
We are still here to help, your questions are perfectly fine..