Maybe a bad relay (in the black box under hood), and more likely, a bad sensor. Theres 3 on the throttle body, but the cam angle sensor or the crankshaft position sensor are more likely culprits based on your comments. Never heard of an Aerio's going bad.
You could also remove the intake tubing from the throttle body to be sure its not an obstruction of air going into the motor, easy to do. Replace the plugs again with ngk v power or the regular ngk's, $2 each, and another easy thing. Be sure they are gapped correctly.
Does your OBD 2 gauge read the history also? Might be a clue there.
1999 Miata, white, hardtop, supercharged, intercooled, 15x9's