Stirlingengineforum.com

...........Same result but your engine will look different. The key is volume of air moved, not configuration of the power ( or displacer) cylinders.

It's best to keep the stoke and bore close to the same. A large bore will also have more friction than a smaller bore with a longer stroke. A larger diameter cyinder with a short stroke will aslo respond better to smaller changes in pressure. It really depends on the type gamma your trying to build. Unless there is a very large difference or you swept volumes are way off, the engine should still run even with non-square piston/cylinder ratios.