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There was a difference in heads from 2nd gen to 3rd gen 3sgte.
First off, the US MR2 only got the 2nd gen 3sgte from 91 - 95. However, the JDM 3sgte changed to a 3rd gen 3sgte from 93 - 98. The internals are essentially the same, with a few slight changes here and there (like the head, and valve cover, amongst other things).
There are a few easy ways to tell which generation 3s you have. First off, the 2nd gen turbo is a ct26 that says "toyota ct26 right on it. The 3rd gen has the ct20b, which just says "toyota" on it. Another way to tell is to look at the pcv valve. It runs from the valve cover to the intake pipe. If there is a catch can in between there, it's a 3rd gen. If straight line, 2nd gen. Also, the 2nd gen has the huge air flow meter on the intake. 3rd gen uses a map sensor and doeesnt have afm.
Either way, most parts are interchangeable between the generations, as they are essentially the same motor. There are a few exceptions, though. Just do your research before making any huge investments.
Hope that helps you out a bit.
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"It's hard to drive at your limit, but it's harder to know where it is." -Sterling Moss
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