the tank must be totally clean inside, so you have the right plan there
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that plastic thing in the petcock nipple is a remnant of the old filter. it's plastic, and should be removed.
get a new, OEM in-tank filter as a replacement. there are different petcock and styles for the 550 so make sure you study the parts list and get the right one. it won't be as cheap as an inline filter but will last forever, and not cause any problems. inline filters can cause inconsistent fuel flow on these bikes.
the fuel lines are a slightly odd size: 5.5mm. for best function, get some of that.
i'm not saying the fuel leve in the carbs actually compensates for a short muffler. but if you change anything in the air-fuel system, it will most likely have impact on some other parts of the same system. so if you change exhaust and/or air filter, in most cases you need to adjust carburation. most aftermarket exhausts are more open than stock. as yours is very short i guess it was meant to be "sporty", meaning more open. also the length has impact on its performance.
as your fuel levels were consistently high, my guess is that someone did that consciously. they may have tried to enrichen the a/f mix to make it work for the exhaust. but that's just a guess.
i think it makes sense to set up the carbs to stock values, i.e. with the correct fuel level. then see what you get. if you want to keep the exhaust, you may need to adjust the jetting which is a more accurate way to tune them then by fuel level.