I would really look for a clean part of the wire to find the true color. Cause it looks like you do have to different color wires from the picture.
The one with brown paint does look brown and the one from the magneto looks red. I would go and connect the like cables.
They both according from the diagram looks to be going the same place. So may not matter but I wouldn't risk it. I have some type of flash back when it comes to the paint...kind of like mine had it too but dont quote me on that.