Why are the coils going bad ever 4000 to 5000 miles

poor grounds, ensure ALL your ground points are clean and greased, there may also be an issue in the wiring leading to or inside the ignitor, perhaps also have your ecu tested at the dealer, sometimes if you haven't reset the programming it believes you're usuing different parts. disconnect the negative terminal on the battery and depressed the brake pedal 5 times. this will allow the memory power in your miatas computers to be reset and go into a "learning" phase, drive the car as you normally would and it should set itself to your driving habits.