The best way to get good sound quality in a Miata is by using headphones or in ear monitors.
I know, this sounds like a downer, really I'm not trolling - this is based on personal experience and, frankly, wasting a butt load of $ in pursuit of a solution.
I replaced the wholly inadequate stock Bose system in my '08 PRHT with the Clearwater Audio replacement drivers and crossovers, along with a very nice Sony head unit and a device to keep the steering wheel controls functional, all professionally installed. It sounded great ... until I started to drive.
There's a fundamental problem with great sound quality and the Miata. The car is a noisy little ******. That's part of it's charm - it's raw, elemental and provides an unparalleled connection between the driver and the road. The road noise, the wheel noise, the engine noise are all part of the experience. With the top up, you have a different set of challenges - the hood that was insulating the noise from the trunk and rear wheels ... ain't there any more! All of the crashes and bangs transmit straight from the rear wheels and the echo chamber trunk straight into the cabin, where the top, now up, helps to trap them!
So, if you really truly are dedicated to getting a good sound system in your Miata, begin with damping and sound proofing and stick with the stock stereo until you get that part right.
I wish you the very best of luck, and please keep us posted on what you discover. Above all else, enjoy your Miata