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I don't think it matters at this point since he'll be making a custom driveshaft. Might as well keep that rx7 diff intact. Unless I'm missing something.
You'll likely have to rebuild the clutch type diff though. I bet the clutch packs are toast.
Actually, I kind of like the idea of using the long nose rear end. It will give you a much more convenient place to bolt a diff mount to, instead of having to build something around the PPF mount on the Miata rear end. Plus, you can use more readily available FC gearing options.