Eh, my housemate has a brand new (about 3k miles now) S2K and it gets pretty shitty mileage. Maybe it’ll get better after it’s fully broken in?
Anyway, I’ve driven a few '03-04 Cobras in various forms of raped-ape (one doing almost 550RWHP and over 600RWTQ w/ a different blower + small shot). They are quick in a straight line, yes. But they just feel like pigs if you even look at a turn. And the quality/reliability. 
S2K’s I’ve driven AP1s and my housemate’s AP2 and I like the 2 better. At the track (and I mean the ones w/ turns… not those stupid straight ones that are only a 1/4 mile long) the AP2’s are more stable and controlable. Somebody correct me if I’m wrong, but didn’t they modify the rear susp. design to correct some of the snap-oversteer when they went to the AP2? Also, around town the 2.2 is better, even though it still feels dead-dog-slow below 5k, it sorta kinda moves the car. A AP1 below 5k is going nowhere… where you going??? NOWHERE.
I think what you really need to be looking at is a mid-mileage '02 Z06. I’m biased as all f00k, I know. But the serioulsy bad-ass hot-shoes have gotten them into the 11s. And if you’re willing to toss a cam in it and some LTs then 11s are easy. They are amazing amazing track cars, and if you don’t mod them toooooo far they DD great and get great MPG. The interior is “meh” but still way better than a Cobra. The dual zone climate control is really nice, the Bose system is pretty okay (obviously not up to aftermarket standards, but until the last couple years it was one of the better stock systems… now days everybody has 23 speakers and 14 subs stock though). You should be able to get a clean, stock, 40k+ mile Z06 for mid 20s.
I KNOW YOU SAID $20k TOPS but really… what is the car payment on the $6k you have to finance??? That is totally worth it. I’d much much rather have a 40k mile Z06 than a 70+k mile Cobra. It’s down right hilarious to me that '03-04 Cobras comand more $ than C5 Z06s. Obviously the Z stickered way higher when new, and in general they are in much nicer shape since they tend to have older owners that take care of them. Seriously, a 70-80k mile Cobra sounds like a bad, bad, bad idea to me. You know that thing has been shit the whole time.
There’s also resale value to consider. C5s have hit the bottom of their depreciation curve. Other than ones that continue to get TONS of miles they really won’t drop much lower in the next 5-10 years. Then they’ll slowly start coming back up if well taken care of. The Cobra will continue to drop and will never come back up (unless maybe it’s a very rare color w/ zero miles).
Drive both a C5Z (which will feel heavy compared to your Miata, but probably much better sorted) and a Cobra and tell me you can’t feel that weight. With the ~700lbs less weight and much better aero you see C5Zs pull Cobras that put down 100 more RWHP.
-TJ