Bigbens6,
I do not envy you on your current predicament, And it seems like you've gotten an earful of the financial reasons for each. Let me give you a little insight on "driving" both cars.
I've done some track days with NASA, and i've also started Karting (which by the way is an excellent way to learn car control and is the most exciting thing i've ever done with 4 wheels)
By brother owns a newer Miata (stock) and I own an S2000 (03' stock). To me the S2k is more of a go kart (tighter steering, your position in the car is further to the rear, higher RPM's, even the throttle is more sensitive) and the Miata is more of a "car" (its more comfortable, nicer layout, sitting a tad bit higher, not as stiff, seats are not as agressive)
Now i've never driven the Miata to the limit, or for long distances. But i will tell you in slow tight corner the miata kicked out on me a little more violently than I had expectedwhen i put the throttle down... I really have to try to get significant oversteer in the S2000 (and I have farely hard tires). Just something i noticed.
I like what people are saying about "its all in the driver," I took a WRX with 150,000 with nothing added except brakes and tires and was overtaking calaway corvettes, mustangs (ans a few s2000's shhhh) and was keeping up with the STI's and the EVO's untill the end of the straights when I had turbo envy ;) But seriously, NASA has great in car and classroom instructors for their HDPE events and they will make you a better driver.
Unless i had a fully prepped Miata and took it to the track to run in the Spec Miata class, and I sold my Honda for the Miata, I would feel as if i "traded down" (please miata lovers dont hate, its jsut my opinion) The S2000 i feel is just a more dynamic well balanced drivers car. Every time i'm in it I jsut want to hit the bens.
On a side note the engine in the S2000 is bulletproof from the factory, and There are a TON of Honda enthusiast out there that are ready and willing to help you out. dont feel like we are hiding somewhere out of sight. If you are planning on using this off track as a pleasure vehicle my s2000 does get 28mpg (the numbers all say 20)
I was looking for a cheaper used Z4 untill I saw this... http://www.youtube.com/watch?v=YWnHPbUMlMU , Then I got the honda (and almost 2 years and i've never had a problem. has 135,000 on it ... I drive A LOT!) hope my 2 sense helped.