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Nope. MZR is a completely different engine family from the FS-DE. Your choices are limited to pre-Mazda3 boxes. The longest-legged box you can fit on would be from the 626 or the Europe-only diesel Familia.
Fifth gear is outside the case, so you don't actually have to tear into it. There are guides on how to do the swap at mazdas247.com.
Oops... I see you're using a 6i. Mazdaspeed box into a regular 6? Should be possible, but I've never heard of it being done. You'd want to see if the final drive is longer than your regular 6, though... otherwise it's a waste of time. Since the box is different to the Protege, any advice covering that box may not apply to the 6.
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