Your description seems to say that the clutch is stuck in the disengaged
position. I don't see how you are going to fix the problem without removing
the transmission from the engine. It sounds like the throwout bearing is
stuck on the shaft in an unusual position.

Usually, you can start a Miata with the clutch in either engaged or
disengaged if the tranny is in neutral, and the clutch pedal is pressed in
far enough to operate a safety switch, or the safety switch is defeated.
You stated that the clutch pedal does not move properly. I would open the
bleeder valve at the slave cylinder and try pressing the clutch pedal to the
floor. If it moves to the floor, brake fluid will normally squirt out from
the open bleeder valve. If the pedal moved to the floor, it sounds like the
slave cylinder, linkage to the tranny throwout bearing (Yoke), and the
throwout bearing are suspect. The slave cylinder may be stuck as a result of
sitting for an extended period of time.  In any event, you will need to
flush the clutch system and brakes to remove the old water contaminated
fluid.