My ca is an LS 6 speed. I had exactly the same problem. I checked
"everything" - I thought! Had to have the car towed to miata dealer.
Took them a day to locate the problem. Wires were chewed by some type of
rodent, probably a fruit rat or Possum. I didn't believe the mechanic but
there was "certain" evidence of the "beast in the engihne compartment.
Guess is was warm and comfy in there. Anyway, cost to fix was $250!

Not to have it happen again, I placed traps and rat bait in appropriate
places. Kept the dog away during the next couple of weeks. No more
problems!