The cylinders determine how much air (therefore how much fuel) is required to turn the motor. An older motor can see decreased fuel economy if the rings and/or valves are not sealing correctly. This doesn't allow it to reach full compression, created a lack of power and fuel economy. That's what was wrong with my original motor. Once of the cylinders was severely leaking, to the point where it would misfire. At best I could get 35 MPG with that motor.
As long as the shop rebuilds the motor to factory specs, and uses quality parts, you can be sure compression will be 100% restored, meaning your engine will be at it's most efficient. Honda did an incredible job engineering the VX motor, I wouldn't go trying to modify the design. There are options such as aftermarket pistons that effect the compression ratio, you could bore the cylinder out to a 1.6 instead of 1.5, etc. But for fuel economy you want to go OEM and run what Honda gave you.
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