[Mr.Fixit]

If it's a regular 60-70's style ford alternator (or replacement) than it has an external regulator. This is what shuts off the alternator when the volts hit 14. That is your problem, the regulator is not turning off the alternator. Swap out regulators first, and be sure the rgulator is grounded to the chassis. This is usually done by bolting it to the inner fender on a steel car, you see the problem with a fiberglass car. Run a ground wire to the case of the regulator. There is very little need for a 100 amp alternator in a cobra. The regular 63 amp jobbers usually work just fine, if too little amps at idle with the fans on, than a 90 amp unit is great.