Advantages of destroking:
-Longer dwell time - means you need less ignition advance, less negative work done as the piston is rising, higher BSFC
-Better rod:stroke angle, less piston/cylinder wall sideloading, less friction
-Smaller displacement, means lower pumping losses
-Lower rotational inertia
Advantages of stroking (or leaving it the same):
-Greater torque
-Don't need to rev as high to make the same power, and friction goes up exponentially with RPM
-Torque is shifted lower in the RPM band
To my understanding, the biggest reason most highly efficient engines are long stroke, is because you have smaller combustion chamber surface area relative to displacement. Larger bores mean more heat loss. However, your bore is going to be the same regardless. That would only be a factor to consider were you looking at, say, a 2.2L long stroke engine vs a 2.2L large bore engine.
It's also worth noting that your bottom end *might* not be your limiting factor for revving. In the Honda K series, for instance, the ~7100rpm K24's use the same valvetrain as the ~9000rpm K20 type R, just with softer valve springs. The valvetrain is therefore almost never the point of failure - people get stronger wrist pins and lighter weight pistons/rods and rev the K24s to the moon. But, in your case, you might have valvetrain issues if you try to raise your redline at all, or at the very least, the valvetrain will become the point of unreliability.
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