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Yes, they are compatible, although slight differences in the gear ratios may be present. Transmissions from MR2s can be problematic though in regards to the shift linkages. The only difference that I can think of would be the possibility of either electronic or mechanical speed sensors in the transmission. I believe though, like the manual counter parts, mechanical and electronic speed sensors are interchangable on these, so reusing your stock sensor should not be a problem.
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'11 Kawasaki Ninja 250R, '12 Mazda2
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