There's a ton of reading out there on the relationship between, and effects of, variations in bore and stroke ratios.
The words below I pinched from carbuzz.com
Unless you are thinking of doing very radical surgery there's not a whole lot you can do to alter the basics of an existing design (if that's what you were thinking?). But you can choose pistons, camshafts and carburettor options, also gearing maybe, that offer optimal low speed performance, just as you can go the other way for a revvy and more powerful one. The bhp differential between a soft- and highly-tuned 650 twin from the same stable and with the same external engine appearance would be maybe 35%, more even - which makes one a nice plodder and t'other a missile (well, relatively speaking!)
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Undersquare (Long Stroke, narrow bore)
This means the piston has to travel further in the cylinder for every revolution of the crankshaft. The longer travel distance increases the piston's speed within the cylinder, but it also increases the leverage on the crankshaft. This leverage advantage of the undersquare engine design results in more torque at a lower rpm. It gives an engine great torque and pulling power even at lower engine speeds. This does limit an undersquare engine's ability to achieve high rpm, also stifling its ability to create as much horsepower as an oversquare engine. The undersquare engine design is typically preferred for towing applications and heavy loads where high torque is paramount over high horsepower.
Advantages:
Higher torque at low RPM
Better low speed efficiency
Disadvantages:
RPM is limited
Higher friction due to longer piston travel
More wear on internal engine components
Oversquare (Bore wider than stroke is long)
Because of its shorter piston travel, such an engine can achieve higher RPM with lower piston speed, ultimately producing more combustion events, thus creating more power at high RPM. Because of an oversquare engine's larger cylinder bore, bigger intake and exhaust valves can be accommodated. This characteristic allows for more air flow through the combustion chamber, allowing the engine to breathe better, bolstering horsepower production. Generally, oversquare engines are preferred for performance and racing applications due to their ability to spin at higher RPM and create more horsepower.
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Although I don't think our post-war machinery was unduly affected by it (just a lingering design hangover probably), the notorious RAC Horse Power formula was responsible for the design of a lot of pretty average engines back in the day, with long strokes to keep down the horse power rating upon which vehicle taxation was based. The old formula went 'Diameter of bore squared x no. of cylinders, divided by 2.5'. So short stroke big bore engines were penalised quite severely in the UK compared to other places and manufacturers had a disincentive to make better faster or more technically-interesting things for Mr Average. Nowadays we're not so one-eyed about things, or should I rather say 'we just tax every little thing there is in existence until the pips squeak'.