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two pieces on what bike I know that on one of my 900rr's I rewire the entire bike with different color electrical wire.. But if you can post some pictures of what you are seeing and maybe some one this site will walk you through the right steps....
if you go to your local honda dealer they can order the conectors for you. They are after market, I did the same thing It costed me apox 20 bucks. it worked well tho. if you need any more info let me know.
Believe it or not there is a kit for this exact repair. I don't remember the part number, but it includes the two piece connector and the connector to the rectifier, with all of the needed wire. Check with a Honda dealer.
I just cut the plug off of the harness for my rectifier. I ended up using splices and sodering them onto the existing wiring. I basically made my own harness. Mine was fried.