The stator or R/R is going to be one of those 95% of the time
Do check the connectors, ensure there is no burning on them and that they are fully engaged & clicked into place.
On Kevin's Touring the ground pigtail connector was burned, so check that - it's about 6" from the battery terminal on the smaller gauge wire.
Can you confirm what R/R you installed? There are a lot of shindengen fakes out there ......
At least in your last couple of posts (havent searched further back)
@mr hunt I didnt see whether you had done the stator check above
Dont worry about number of pins - pretty sure your OEM harness doesnt have three wires on black connector so centre pin question is moot