You will be checking the system (or regulator) while it is working configuration. Yes, everything will be plugged in. You may need extra jumpers to access some points of the system with probes. Either that, or component substitution with known good, or continued guessing...
The plug that contains the yellows (Alternator output), also has the rotor or magnetic field coil wires. The voltage on the field coil wires determines the output strength of the alternator. Higher voltage on the B & W make the yellows put out more power.
If your battery is still not being charged, your regulator may not be passing voltage to the alternator.
It is a process of elimination. You have checked the rectifier and found it good. You have corrected the field coil connection to the regulator.
Now you need to know if the regulator is still performing.
Or you could check the yellow wire connections to the rectifier. If you find the same high resistance indications that you had on the black and white wires, that can be cause for failure, too.
The regulator and wiring are the last major components of the charging system that you haven't "proven" with test devices.
Alternator rotor -- √
Alternator Stator -- √
Rectifier -- √
Connection from slip rings to regulator -- √
Regulator -- ?
Connection from stator to regulator -- ?
Connection from key switch to Regulator -- ?
Connection from Rectifier to Battery -- ?
Once you have checked all the system components and assembled them into a system, it must work as it did originally.
Physics demands it.
No hand waving required. 
Cheers,
Found the SHORT... It was the wire connector at the base of the Brush Holder. It was accidentally pinched when it was put back together.
Below here is the Regulator Test as requested...
This Tests is at the Battery Terminals:12.75v Bike OFF
12.50v @ Idle
14.36v @ 2K RPM
14.40v @ 3K RPM
14.40v @ 4K RPM
14.40v @ 5k RPM
This Test is from the Black and White Terminals at the RR:12.2v @ Idle
11.3v @ 2K RPM
7.5v @ 3K RPM
6.4v @ 4K RPM
5.6v @ 5K RPM
How does the results look Two Tired??? I assuming it looks OK!!!
I did also find out the Bike is also running on 3 Cylinders only...The outermost left cylinder if you are sitting down.
That another project!
I cant thank you guys enough on helping me troubleshoot my issue.
