Paullito, you can just cut the second headlight plug or cover it with tape and hide behind the headlight, if there's enough space. You don't need to buy any wire if you have Fz6R headlight wiring. You can use its speedo socket without cutting. Just take out all the pins that goes to speedo socket. Also take out the pins going to the original Fz6 speedo, swap them. And you have a nice clean wiring. May be you can use Fz6r wiring directly if sockets fit.
Also as TownsendsFJR1300 mentions, you need to add a single cable coming from left hand headlight switch to your new single headlight.
As i write these, it looks very complicated, but it's not.
To remove pins, you can use a needle, or little screw driver. Here is a video:
[video=youtube;S9xeg_3eREc]https://www.youtube.com/watch?v=S9xeg_3eREc[/video]