Ah.. I missed the convertible part.
Regardless of the location, i still think it's that wire. The wire colors, and that particular connector are unique to fox speakers. Also, keep in mind ford would try to use as few harnesses as possible, so the speaker wiring could be long enough to reach the convertible location, and the hatch location in the rear. That wire certainly does look like it's long for a reason.
I also seem to vaguely remember the rear wiring harness for a fox travels down the driver's side, wraps around the taillight panel and then the tail of the harness heads towards the RH speaker with that being the last wire on the harness. Is that's the case, then it just looks like the wire wasn't extended all the way properly.