I believe the follow paragraph from page 74 of the 2024 SCCA Solo Rulebook applies to your question regarding the exhaust:
Option package conversions may be performed between specific vehicles
of a particular make and model, but only between configurations from
within a particular model year. Such conversions must be totally complete
and the resultant car must meet all requirements of this Section. These re-
quirements are not met by simply pulling a fuse to disable a feature which
distinguishes one model from another.
I believe this would be considered legal, however everything else about the California modification would need to be converted back to 49 State car. This would be to follow the rules as written by the SCCA, however locally if you discussed some fellow local WSCC stock class competitors about only swapping the exhaust I don't think you would have any problems as there likely no performance gain from missing out on removing additiional California specific items, unique EGR, maybe? There's nothing in our local rules that would restrict US cars from competition either, however if you planned to run at an offical national SCCA event this could be a problem, hope that helps.
Regarding the wheels, your wheels are based on what the car originally came with from Mazda. For example if a 2000 Miata Sport (not sure which model you have) came with 14x6 +42mm offset. You could run a 13x6, 14x6 or 15x6 wheel. Offset can be +/- 7mm from the OEM size as well to accommodate some wheel models. Wheel width however cannot change from the originals wheels the car sold with new. You cannot pick and choose from any other Miata year or model to select a wheel size.
15x6 with 205/50/15 tires is like the most cost effective, best performing and most common wheel setup available for ES Miatas that came with 14x6, 15x6 or 16x6 wheels.
Regarding the 110-178hp Miatas on 14 to 17" wheels comment all running in the same class. SCCA car classing offers every car a class to participate, this however does not guarantee all cars will be competitive in their respective class.
Hope that helps!