I suppose it does make sense that if you're increasing the stroke it wouldn't be as easy to rev as hard. Also, you aren't really increasing the volume of the engine that much % wise once you are adding only a few tenths of a litre.
How did the GTR respond to the reduced capacity? I think it was Nismo that reduced the capacity of a VH45DE to 3.5L and it revved like an F1 car. Your GTR already is a very revvy machine, so it must have been even better at 2.4L. If I remember correctly, you were having trouble shifting at very high revs at some point (my memory is bad, sorry). Did it make shifting harder?