Unfortunately it could be the dreaded crank key way failure. I am going through this now on my supercharged 1.8l. Look at the crank pulley as it idles and see if it looks wobbly. If so, try spinning it by hand with out any belts. If the 4 bolt holding the pulley are on tight, but the pulley wobbles, you've got a bad key way.
Search miata loctite fix.