Hi again.

The jumper wire should be for diagnostic purposes only. The problem is that Ford's wiring is still there. If you have a problem with power not making it to the flasher, but, everything else on that fuse works, then the problem is almost certainly with the wire itself, and there are only a few different problems that an actual wire can have, and they all come down to a short somewhere. If you just bypass it totally, then you still have a live wire with a short in it behind the dash. The short could be contained because the other wires around it are acting like insulation and preventing it from sparking and starting a fire behind the dash, but, it is also possible that the short is not being insulated like that. I would definitely either go ahead and track it down, or, at least, separate that wire from the back of the fuse box so that it doesn't have power on it.
