I have a 75' cb550f. For the past year or so, I completed the exaust, carbs, filters about month go. So, I should have some good advice for you.
I have been on ebay and other sites just about every day. Finding an original cb550f muffler is difficult....they are rare. If someone is selling one, they are usually rusted in two places...on the bottom where the muffler attaches to the header and at the back end around the exhaust opening. You can get one for under $100.00 if you look long enough, it will most likely have one hole minimum. If one does show up in mint condition, it will be selling for around $400.00 to $500.00....unless you get lucky. I got lucky..fortunately.
There are a few aftermarket slip on mufflers for this bike....but none that look too close to the original. The aftermarket slip ons are usually alot shorter and have a different shape than the original.
I have cone filters on mine, they are emgo 35mm. The rubber on them stretches to fit your carborators. They fit the bike nicely, they are smaller than most cone filters. If you get the larger cone filters made by emgo they will not fit between your carbs and the frame. The box from emgo even says they fit cb550 bikes...but they hit the frame. There were some past posts regarding cone filters on cb550 bikes.
Jet sizes are mostly going to depend on the type of muffler you end up getting. The more open the exhaust is the larger the main jets. The original main jets are 98 but 100 will work with the origial exhaust also. I have 100 main jets. Mine are Keyster. They will run around $60.00 for all four.
Sound like I am about a year ahead of you on the cb550, so if any questions come up, feel free to ask.