Okay, we're still not finding a root cause.
Let's go back and measure the field coil resistance again. This time measure it from the terminals the would normally connect to the regulator, the White and Green wires disconnected from the regulator. If the measured value is close to the 7.2 ohms required. Then check the stator windings once more from the connector pins that the rectifier plugs into.
Between any two (of the three yellow) should read very low 0.2 ohms which will be very hard to read acurately with your meter. However, there should be some very small difference in scale readings between a probes joined together reading, and probes on connector pins reading. Also, make sure none of the yellow wires ever gets continuity to the engine case.
If something hasn't popped up as irregular with the above tests so far, then get yourself a piece of wire 18-14 gauge, and bind one end of the wire to the battery positive terminal. The other end of the wire you are going to use to inject or directly connect battery 12 v where is it supposed to be connected, bypassing hte bike's wiring.
With the alternator spinning about 3K RPM inject your 12v probe directly onto the white wire at the regulator.
Monitor voltage across rectifier red/wht and green and also at battery terminals with and without the jumper. Note the four readings taken.
If things still aren't looking better, then measure the AC output (circuit connected) with and without the bridge wire.
If you still can't get over 13 V at the battery, then try using your 12 v injector to connect the battery directly to the rectifier output Red/Wht connection, bridging the bike's wiring. This can be tricky as you may have to unlatch and push pins out of the connector and reconnect externally to effect this bridge connection. If you STILL aren't getting the charging power to the battery after this. A similar technique can be used to bridge the Ground returns between battery, field, and rectifier.
The idea here is to verify the major components are working and trace down wiring issues later. Be very carefull with your long wire battery probe. If it contacts any frame or motor components, it will short the battery and become very very hot. The battery voltage won't hurt you but the heat it can generate will. I might clamp a vise grips near the loose end of the wire as a handle/weight, so it will stay where it is placed and not whip around on its own. Don't expose any more of the wire end than is necessary to make the minimum contact.
Remember all this bridging is harmless if you apply to the correct connection points. The wrong ones will fry something, I'm afraid. So, double check and be certain before making bypass contacts.
I'm running out of ideas on how to do this remotely. Probably take me 5 minutes to diagnose in person. However, visual cues are lacking through this medium.
Good luck!
