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Should not be a problem. But I am not 100% sure. I know at some point they went to bigger flanges on the 997 gearbox but I don't think it was until 2010+.
996 GT3R's had the bigger flanges and then some 997 RSR's also came with the big flanges.. these "big flanges" are the size required to run Metalore axles...... length and spline wise most will work in any cup / r, rs, rsr configuration.. only the inner CV joint has 2 different options... but rare to see the bigger unit..