Oh hey, someone working with a MR-S. I used to have 2.
The front cooling is definitely a good place to look. Ducting the exhaust might be too much effort but the intake definitely could use some modification. If you can take out the grill, it should be easy to take some plastic sheet and foam and make a smooth duct with a smaller and more efficient opening.
I remember thinking about how to make the exhaust a bit better and my conclusion was that you can remove the stock plastic piece and replace it with a flat plastic panel with a thin slit cut in it and an angled duct above.
As far as the rear, I would just toss on the longest spoiler you can find (if it doesn't need to look really good, this is pretty easy to DIY:
https://auroraautodesign.com/product...nb-miata-90-05)
You can try to mess with a diffuser but the lack of OEM paneling suggests to me the results may not be great.