1999 Miata pindicates 17 volts when running

I think the problem still might lie in your alternator. for some reason it is overcharging.

Turn your headlights on and check the voltage again ... ... If that alternator is still putting out 17 volts, you have one helleva alternator. Most alternators will give you between 700-800 watts and if that voltage has not dropped with headlights on you are hitting close to 340 watts ... without a correction you will soon start having premature failures of everything from Headlights to coil-pacs Most cars run a little over 14 VDC. ... Most alternators have a built in regulator so it gets changed when the regulator gets changed .... however, in todays world where the regulator may be a separate part # ... I would not assume anything

Tom is right about that! On some models the voltage regulation is shared by the ECU. There are also some cars where there is no voltage regulator in the alternator, but it is entirely controlled by the ECU.