Stroking the motor is totally up to you, look up people who have done it and what they say about it. All i know is it will lower how high you can rev the motor, so it depends what kind of use you want for the motor, dd or race.
As far as the heads go, the z6 gives more room for bigger domed pistons, but the y8 is supposed to flow better and has quench pads to give a better burn, but limits how big of pistons you can run, unless you run a thicker head gasket.
I'm buildin up another HC z6 myself so i know a lil bit about this, if you have any more questions let me know. also check out dseries.org, lots of great info over there.