OK, I'm installing the directional turn signal mirrors from American Muscle. When making my connections to the SJB, I can't find the Dark Blue/Orange wire for the right front turn signal. Is there any chance Ford would have used a different color wire?

I have the driver's side wired (Grey/Black), just can't find the passenger side to splice into. Has anyone else done this? Any troubles?

 

Keep hunting. I installed them in my '06 and it was fine. If you have a Hanes manual, you can also look up which wire it is if they have changed the wire colour.

According to my Hanes manual for Mustang 2005-07, page 12-31/32 you are looking for:
For front turn lamps
Left = Grey/Blk
Right = Dark Blue/Orange

For the rear turn lamps
Left = Light Blue/Orange
Right = Red/White

Before you make any connections you can use a tester light to make sure you have the right wire. That's what I did.

Good luck.