Is there some sort of mathematical formula, which determines appropriate throttle body size based on other components in the system? Further.....I get the 55mm throttle body size, and I know what a plenum is, but I'm trying to figure out why on my TB the plenum is 3mm larger. Is there a venturi effect, which increases the velocity of the air by having a larger plenum vice TB?
Generally.....I have noticed alot of folks using 62mm TBs on 110cid engines, 50mm TBs on 120cid engines, and in my case, a 55mm/58mm TB on a 117cid engine. It appears, from that structure, that those with more displacement are using smaller TBs...........which makes absolutely no sense to me. 
The general answer is any of those sizes of TB will run well with any of those displacement motors. The dyno may see some differences - buy your butt likely would not...
The difference between bolting on a 58 vs. 62 mm throttle body on the same motor is minuscule for general riding around...
When my family raced (road racing), we would have entirely different configuration motors and carburetors dependent upon the type of track we were running on ... and for this "all out" application - it mattered. 750, 830, 850 carbs - different jetting, different power valves, different flow work, ect. - dyno tuned for the exact type track we were running - and then further adjustments for the weather of the day, ect. The combination of heads, cam, intake, carb would be very different from a slower "torque" track to a faster "horsepower" track. Same with drag racing...these variables are incredibly important...
But for casual bike riding - you would be hard pressed to notice much difference from one throttle body to the next.
If you had a stack of throttle bodies available when your bike is dyno tuned - and you wanted to take the time to try the various combinations on your motor, you would likely find a throttle body best suited for your exact cam/head/exhaust combination. But to the seat of your pants - anything from say - 52mm thru 62mm - would provide a similar result.
So - no - there is no mathematical formula....it all goes to the "combination" of components that you read so much about. Your throttle body is just one piece of the overall puzzle - and selecting the right one depends the rest of your puzzle - combined with how you ride your ride!