David, speaking only of naturally aspirated engines, the over square method of achieving a set cubic inch goal will be more reliable. Increased rod angle is the biggie, with a taller stroke. The more rod angle you have, the more wear you put on the cylinder wall, and the piston rings/skirt, and it also puts more heat in the engine from friction, which is a no no. A bigger piston will run cooler, all things being equal, due to more surface area for oil splash to cool piston from bottom.
These are things to consider if your building a high rpm endurance engine, which your not, so I say build what you'd like, and enjoy it.
Fun fact...in two absolutely identical engines, one having aluminum heads, the other having cast iron heads, the engine with cast iron heads will make more overall power, due to being able to hold heat in the combustion chamber longer...
Totally off topic, but worthy of discussion also. Logically, you'd want aluminum heads over the iron heads, due to weight, and where the weight is at in the vehicle.
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