These what is the best questions always cause some different opinions. Everyone has their favorites. In general, I think a Miata may be a bit underpowered for the Pro cup. You can upgrade it a tremendous amount, of course, but I've geberally avoided insane upgrades.
I'd try the TVR Griffith 500 or, maybe, an S2000 (if you have it, the Spoon would be good; not the race car).
Modifications? As always, I'd start with tires, then put in a full racing transmission so I can adjust for the tracks. Then probably upgrade the exhaust, clutch, flywheel, racing chip. I then tend to see how a car does with these changes before going for the big NA Tune Up or Turbo upgrades