What is the difference in cost between .020 over pistons and .040 over pistons? This should probably be your driving factor.
With the Honda's there is no difference in HP gained between .020 over and .040 over, but the .040 over pistons cost $400 more. Not exactly worth it.
Motor performance is not directly proportional to displacement. There are other things to consider, like the weight difference between the two piston sizes. It'll probably be insignificant, but it is something. Depending on how high your motor revs it may be worth more to have the lighter pistons.
Your biggest gains are going to be from the compression ratio. Seeing as either way you'll end up with 9:1 it might not matter which piston you go with.
Since you said money doesn't matter build two motors and dyno them. Then you will know for sure.
Basically no one can answer your question without knowing a ton about the motor you are building. Each motor is going to be different and all you can do is speculate. In all honesty, cost of the parts and ability to rebuild the motor should be your driving factors.
Jamie
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