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One may have a different revised runner. I would think that you would be able to score the 243 LS6 heads cheaper though since all the new LS2 stuff has come out.
They are the same heads. However, the valves do differ. The LS6 heads come with sodium filled valves and the LS2 heads do not. If you are looking for some 243 heads, we have some great deals on them.