It seems to me that special editions are the way to go when it comes to Miatas. Just as an example, mine is a '99 10th Anniversary Edition. I wanted ABS, the 6-speed transmission, the sport suspension and the factory body kit. The 10AE has all of those things standard except for ABS (it was an option, mine has it), plus it has a unique color, special interior, and a few other neat bits. I could have tried to search and find an LS with those features, but the 10AE is a nicer overall package anyway.

I see no need to order an exact match for what you want. Well maybe on a regular Miata, but not a Mazdaspeed. There are essentially no options for the MS Miata. You pick red or dark grey, cloth or leather. That's it. If this dealer doesn't have one but you like them and want them to get the sale, then ask them to do a DX (dealer exchange) with someone who has the car you want. But yeah you should be able to find either interior option in either color with relatively little fuss.

If you want a hardtop, the body is the same as the regular Miata. So as long as Mazda is selling them in the MS colors you should have no problem. Worst case scenario you buy a hardtop in another color and have it repainted. That's a question I would pose on miata.net since that's a far better source of information than little old me.

I think they're not moving off the lots because Miatas in general aren't selling. It's not a practical car and most people who are not passionate about their vehicle can't justify a little 2-seat roadster with a tiny trunk. But if you get past the overall objection to the Miata itself, the only reason I see not to buy a Mazdaspeed is if you can't afford it (I fall into this group), you really are hung up on some color that the Mazdaspeed isn't offered in and are willing to give up on the turbo, and sort of going with that you want to do your own turbo and want a particular color to go with that turbo.