I believe the intent of the rules does mean you can run any size rim that came on any year NB Miata. Even if it only means what came on 99's, I do know that Sport editions and the 10AE came with 15X6. Not sure if the extra 1/2" is worth the cost, it wasn't to me. I also autocross a 99 Base Edition in C-Stock. I now have 3 sets of rims. A set of NA spoke (minilite clones) that are 14X5.5 w/Falken Zeix (the street tires), a set of original alloys in 14X6 w/Falken Azenis and a set of 14X6 Enkei's w/Hankook R-Comps. The R-Comps are 205's so wider does fit stock. Thought about getting a set of 15" rims for tire choice availibility but 14" tire choice isn't bad yet and affordable. Got my extra sets for reasonable price, couldn't pass up the NA wheels at $50 for the set w/tires.

Back on topic, that would depend on whether you think its worth the extra cost to you. IMHO, I don't think there would be enough of an advantage to warrant the extra cost. Me personally, for the price of 14" tires vs 16" tires and how often I buy tires I'll stick with the 14".

I went over to www.miata.net and found this for 1999 Miatas
http://www.miata.net/faq/america/1999.html
It seems that to get 15's in 1999 that they only came as part of a package which are...

Leather Package: Popular equipment package items plus tan leather-trimmed upholstery, tan vinyl top 15-inch aluminum alloy wheels and BOSE audio system. All leather package Miatas with automatic transmissions come with ABS.

Sports Package (manual tranmission only): Sports suspension with Bilstein shock absorbers, rear spoiler, front air dam, 15-inch aluminum alloy wheels, Torsen-limited-slip differential, strut tower brace bar and 3-spoke Nardi leather wrapped steering wheel.

If you have 14" alloy then you likely have the Touring Package which is:
Touring Package: Variable-assist power steering, 3-spoke Nardi leather-wrapped steering wheel, 14-inch aluminum alloy wheels and power door mirrors.

Based on the rules of SCCA you can add packages to your car but if doing that you have to add the ENTIRE package. What that means for your year to get 15's you need to add: rear spoiler, front air dam, 15-inch aluminum alloy wheels, Torsen-limited-slip differential, strut tower brace bar. Dont worry about the Bilsteins, they can be claimed as a wear item and replaced with any shock either a better shock or worse and still be in the letter of the rule as long as the ride height remains the same.

Equally, you could get 15's by adding the popular package and leather package but that would cost even more.

Stock is not the only class. Look into the Street Touring class as well. The rules are different there.

Figure out what package car yours is and what wheels it came with stock. You have to run that size unless you can switch to a different level of trim. You won't be able to run 16's since they weren't offered in 99, but 15's are better anyway. If you are just starting out, and are not winning, likely you could get away with running some 15x6's on a touring package and nobody would care. If you start to get more serious and beating people, you would have to make sure you have the correct wheels for your trim level car.

Street Touring does allow a bit more mods but not a lot. And the down side to that is the only Street Touring class a 99Miata NB fits into is the new STR class. Also in Street Touring you have to run some type of street legal tire. Like Azenis for example plus a few others. But in C-stock you can run R-comps if you want.

Decisions, decisions. I went through this myself with my car but that was before STR came about. Now that I run R-comps I don't want to go back to a street tire to run STR. Plus there are a few other stock mods I have yet to do.