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I too came from a 3.8 RS and also feel that the 4.0 is much more dialed in, and the engine is so much more powerful than the numbers suggest. The jump between the 4.0 and 3.8 RS was bigger than between my 997.1 non RS GT3 and the 3.8 RS.
I have both a 3.8 and a 4.0. For me, the 4.0 is almost more comfortable as a daily driver. The power is soooo smooth all the way up and down the rpms, it really is fun to drive. They really are different cars.
Drives like a Caddy was my first thought ;-) much nicer on the street, specially with teh M&M exhaust for some sound low RPM and a little quicker at the track too.
Unless it's different in the US, the problem I have with getting a 996 cup is finding a "nice" one. One with original low hours. Any way you look at it, the tub ages, and things wear out.
If $$ was possible for me, I would get a nice 997 cup and possibly replace gearbox with a 996 cup box.