Typically its a matter of trial and error.
What you need to think of is the air fuel mixture, the more air you are pulling in with these pod filters means you need more fuel to mix, meaning larger jets. If you then put on new muffler that means you are exhausting more/less, meaning a change in back pressure.
Generally if you are using pods, and opening up the mufflers to something that is more free flowing (like shorties) you should step up the pilot jets (1, maybe 2 sizes) and the main jets ( maybe 2 sizes to start).
After installation you will then be able to see if you have a lean mixture, or a rich one, by watching if the RPM needle hangs anywhere and by checking the plugs, and by using your eyes and ears.
If its good on ideal, but hangs when you rev it, your are lean, and will need to go up. If it seems to be okay, but just not right and the plugs are really dark then its rich and you may need to go down.
That is just the basics, as it gets much intense when you start playing with your needle clip position haha
Somewhere on this site is a post or a guide that details how to go about re-jetting. Its not TOO difficult and to be honest when i did mine i just went 3 sizes up on the main, 1 on the pilot and called it a day lol It wasn't ideal, but when I could get it running- it ran haha