With that being said I tested the resistance across the copper windings of the rotor and got ~ 5.5 ohms.
That's a reasonable rotor resistance for a field coil. I don't know the exact spec for this bike, though. Still, it ought make enough magnetic field in which the the stator can produce power.
i then unplug the stator from the R/R it had 5 wires - 3 yellow, 1 black (hot), 1 white (neutral). i tested the resistance across the black and white and got off scale reading.
The black and White wires function is to deliver battery voltage to the alternator (to make an electromagnetic field). I can't determine if the plug you checked is wired to the alt or to the R/R. If it's the plug to the alt. it should read pretty close to the 5.5Ω you measured at the rotor slip rings. If it's the plug wire from the R/R, and you R/R is a solid state device. You may need a meter that supplies enough voltage to make a diode or transistor junction conduct. If the voltage provided by the meter is too low, it may well read infinity as the regulator output will not pass any current for the the meter to measure. Digital meters usually have a diode symbol on the knob setting scale for testing active devices. The symbol looks something like this -|>- . However, I don't know the internal design of your regulator. So, any reading made to the output of that device is speculative as to correctness.
You'll probably have to measure voltage on the Black and white wires with then properly connected and the key switch on. For any battery reading below 12.6V the black and white wires should have very close to whatever the battery reads.
Across any of the three yellow wires was about 1.3 or so.
Probably nothing to worry about here. Technically, this reading should be lower. But, you need a meter that is accurate for lo ohms, and you need to subtract the meter's own test lead resistance from the meter's reading.
The last test I grounded the common probe to the engine block and used the red probe and a spot tester.
The engine block and the battery NEG terminal should be the same electrical potential. You should gain confidence that this connection has integrity. In fact, you should gain confidence that any green wires have good electrical conductivity to the battery NEG terminal, too.
Cheers,