First, try breaking it down into several categories: although there is a little bit of interaction between the inlet tract and the exhaust, using the components you are speaking of, it's not much. If you had, for example, a wide duration cam or 11:1 compression on a stock cam, then they start to interact more, and make it more complicated.
The intake tract: don't think in terms of car carbs. Those are constant-vacuum devices: these are pulse-feed carbs. They act differently, by a stretch. At idle speeds, the suction pulse is very short, so it must also be quite rich or else there isn't enough fuel to burn. But, just off of idle (about 1250 RPM) this must change. At idle, the mix is about 12:1 A/F, at "throttle crack vacuum", or the beginning of low range control, it has to drop to 13:1 A/F or the engine will blubber and then lurch off as it cleans itself out. This transition is controlled by 2 things: first, the idle air screw setting and second, the float level. Always, always, start there, with the factory settings. Otherwise, it will either not idle, not return to idle, or will have a hard time getting up from idle. Most of our air screws' seats are widened a litte from the years, so consider turning them inward slightly (1/16 to 1/8 turn) over stock to compensate for this wear issue.
As soon as you reach 1500 RPM, you begin to enter the region of the cutaway on the slide of the carb. While you can't do a lot of changing with this part, if the float level is too low it will fall flat on its face here. The air screw still controls the mixture until 2500-ish RPM under normal riding, in gear. If the spark advancer is advancing too fast because the springs have become annealed (soft) from the heat cycling, this also makes them fall flat. Stiffening up the spring(s) helps, specifically, here.
As you approach 3000 RPM, the needle position in the slide starts to have more authority over the idle air screw. The air screw is 'out of the mix' by 3800-ish RPM on the oversquare bores like the 500/550. Now, you are running on the mixture set by the needle position, slide cutaway, float level, and the permissiveness (or not) of the air filter material. This remains the picture until you reach more than 1/2 throttle, or about 6500 RPM in gear with the 500/550. This is the dominant riding setting range.
Above 3/4 throttle, you are at the mercy of your inlet filter's breathing ability and the size of your main jet. At this point, the exhaust, if it is restrictive, starts to improve on the situation: if it is not, you are running right against the jet, so to speak. Backpressure at higher engine speeds causes less intake charge loss during the overlap time between exhaust-and-intake stroke TDC (aka 'overlap'), when the inertia of the incoming air-fuel mix actually pushes across the top of the piston for a short time, putting unburned gas into the exhaust as it fills the now-growing chamber while the intake stroke starts. If you have some backpressure, this helps slow down the speed over the top of the piston, which reduces the speed over the main jet in the carb throat, which in turn richens up the mix a little bit and lets the needle's position control things. If the air moves too fast here, it sucks the needle dry, and essentially "tops out" the mixture early. Then, increasing the mainjet, but dropping the needle so as to preserve the midrange throttle control, is the answer.
That last statement, I find, is where most folks go , "Huh?". So now might be a good moment to explain how these carbs actually work, if you don't have my book. First thing: engine vacuum does not suck the gas up the jets and into the engine, period. Instead, what happens is this (which you can verify with Bernouli's laws): the suction in the carb throat accelerates the air there via the narrowed venturi area where the slide lives. Note that at the back of the carb is a larger bell-shaped area where this air arrives: this air is at [nearly] atmospheric pressure. Inside the venturi, it is about 25% less pressure, because moving air is lower pressure than stationary air. So, those little ports you see at the mouth of the bell, which go down into the mainjet and idle jet mixing chambers, are being fed this high-pressure air, while the emulsifier chambers that sit atop the mainjet and idle jet have been exposed to the lower-pressure air in the venturi. This makes the air at the bell push its way down into the emulsifiers and up into the venturi, to try to balance the pressure. Meanwhile, there is a vent for the bowl that goes directly to the outside air: this is at even HIGHER pressure than the bell area, so the bowl is busy pushing fuel up those jets, to the mixing (emulsifier) chambers all the while. This is how these carbs mix air & fuel. The suction then just scoops up the little squirt that is laying, wet, on the floor of the carb at that point. In essence, each suction pulse of the engine gets the PREVIOUS suction pulse's gas. It's always one pulse late, which is called "throttle lag".
Now...in all this, note that the exhaust pipe backpressure plays very, very little into the game until it either disappears altogether (ths increasing overlap scavenge into the pipes, losing it from the cylinders), or becomes so much that the engine can't spit out the burned gases. In other words: from a full set of 4-4 pies to a straight-thru 4-1 header collector with drag shortie length, there is less than 3% possible change, with the stock cam. So, don't fret the exhaust pipe situation.
The intake is another story: the stock air box makes VERY still air, so it is at the highest possible pressure to enter the carbs. This presumes the whole tract is still there, and the paper air filter is not damaged by moisture, which plugs them up like they were a UNI filter. (K&N is the very best solution, hard to find for the 550, though). The UNI foam filters tend to lower the pressure at the bell of the carbs, because it is a restrictive filter if it is over-oiled, and it takes very little to over-oil them. Typically, I soak them in oil, then wash them out with soap and water, dry them, and THEN install them, just like that. This seems to at least let the top RPM come out of the bikes.
When you install pod filters, the air at the bell is moving in a dozen different directions, tumbling over the lip of the pod's mounting flange, and, when moving down the road, suffering from the shear angles of the air bouncing off your legs and tumbling over the top of the engine. This seriously disturbs the needed still air at the bell, hence the problems that ensue with mixing, with those filters.
So, all this said: for a given non-stock air inlet tract, there will be zones of too-rich and suddenly-leaner mixtures, interacting with each other. You physically can't fix that. What some have done is to simply make the whole range so rich that it doesn't duffer the fall-on-its-face transition when going from too-rich to normal (or lean) ranges, then they have to live with the sparkplug fouling problems. But, it runs. So, you will see folks recommending as high as #130 mainjets on the 750 or #120 on the 550, which is enough fuel to run a dragstrip with, IF you had a 60kV CDI to ignite it with: otherwise it will run, but will darken the plugs, soon. For casual rides, this may be OK. If you ride it to work every day, or try to tour with it, not so much.
