Since birddog addressed the bore, I´ll address the stroke:
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But when you stroke it you are getting more air/fuel into the combustion chamber as well as compressing it more.
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[/TD][/TR][/TABLE] Generally, to stroke an engine you´ll need special pistons (with a shorter distance from the pin to the top) or to have your stock pistons milled down, if that´s even possible, to keep them from hitting the cylinder head. So the compression ratio can be decided upon by what pistons you choose.
One problem with stroking is that you reduce the rod/stroke ratio which means lower VE (volumetric efficiency). This is why F1 cars use long rods and short stroke. A short stroke means less movement of the piston (lower piston speeds) while the large rod/stroke ratio means that the rod will leave the piston and meet the crank at more efficient angles (more straight up and down than side to side). This allows for higher revs and better efficiency. When you stroke you´re forcing the piston to move faster and causing the rods to travel through a larger circle putting more stress on the crank and the bearings... although the additional travel of the crank also means more torque.
So, if you´re planning on building a high revving racy engine, avoid stroking unless you plan to deck the block for additional rod length. If you want better driveablity around town and like laying rubber strips, you may want to consider the stroke.