I don't know the way the R/R connectors are setup on this bike so I will give a generic test method, you may have to modify it if all the wires are in one connector. If the connector(s) have SIX wires, stop here and let us know. The sixth wire is usually a battery voltage sense wire and trumps all other testing and should be verified first. And another thing, Honda stator wires have been notorious for melting connectors and damaging wires and pins. The very first thing (after counting wires) is to carefully inspect the stator connector, the wires where they are crimped to the pins and the pins.
A duffer at home with a generic multimeter can't test a stator's resistance correctly. The stator windings have less resistance than the multimeter leads. What you can check with the meter is to verify that there is infinite resistance between the stator wires and the ground - there should be >10 meg ohm to ground. If it is bad you won't have to worry about an ohm or two, it will be significantly different.
A duffer can use a multimeter to check the AC output of the stator and determine the health. Unplug the 3 wire connector, set the meter for the AC scale and the range sufficient to measure up to 70 volts. With the engine idling, measure the three pins, any pin to any pin - all reading should be within 1 volt of each other. This is more important than the absolute value. Now run the engine up to 4-5k rpm and repeat the test - all readings should be within 1-2 volts of each other. If the stator is bad, the bad winding(s) will be very different from the others, you won't have to worry about half a volt, you will be seeing many volts and at 4-5k rpm it could be 20-30 volts different. If the stator passes this test and the resistance to ground test it is almost certainly good.
Now plug the 3 wire connector in and unplug the 2 wire connector (Red & Black wires). With the engine idling you should read >14.0 volts DC (remember to set the meter scale back to DC). If it passes this test the R/R is almost certainly good. Plug the connector back in and back probe the connector and measure the voltage again. It should be 14.0 volts or greater. If it passes this test everything at the R/R is working and good.
Now go to the battery and read the voltage with the engine running at idle. The reading at the battery, while probing ON THE BATTERY TERMINALS, not the battery wire connector should be within 0.2 volts of what you read at the R/R. If it is more than 0.5 volts you have a wiring problem.
By this point you should know with some confidence what the problem is. Let us know what is out of specification if you need help running down the problem.
Be careful when testing the stator and don't short the pins.
