I have three red wires (labeled R1, R2, R3 in attached picture) coming from the rear of the loom.

Q1:  Should all 3 red wires have connectivity with each other?

Q2:  Which wire (R1, R2, R3) should connect directly to fuse?

Q3:  If the answer to Q2 is R1, how/where should R2 and R3 be attached/connected?

 

Pictures not working at the moment.

From memory, two of the wires have female connectors and one has male. Fuse holder sits between the two females and the male connects to the positive terminal on the battery.

glad to send over a picture jmckinney if its helpful

Thanks for the reply!

See new attached pic/drawing...is that how you're describing?

And please advise if my pics are not visible

Pics are not visible, there's an issue with posting pics. If you want to post pics you have to use an image hosting site.

This has to be one of the most asked questions here.

No, all three reds do not have continuity with each other.  The male connector red (goes to battery) is simply a short wire wrapped in the harness.  The other end is one of the two female connectors. So there is continuity between male red and one of the female reds.

The other female red powers the bike. 
 
Fuse holder connects between the two females.  See pic of factory fuse holder here:  www.partzilla.com/product/yamaha/55K-82150-01-00

It's genius in design...  if battery is disconnected from male harness connector, female connector on battery + protects battery from short.

Exposed male wire that plugs into battery is protected charges battery and could short if grounded with engine running...  but fuse would protect it. 

In fact, every connection is protected from damage caused by short to ground if a connection comes apart (or is unplugged) by either a fuse or a female connector. 

MarkT, can’t thank you enough…much appreciated.