The 550 carbs don't have an enrichment device for getting fuel into runners when the throttle is quickly opened and the throat pressure increases. It relies on an over rich idle mixture for throttle response and even then it will not take drastic snap open throttle without the dreaded wheeze.
It will take 1/2 throttle changes when properly adjusted.
You're right pods filters are better for the engine than nothing. But, they change the throat pressures in the carbs, which effects how the fuel is drawn from the jets. Almost certainly, you will have to enrich the slow circuit to regain your throttle response. The screws you have are air bleeds. Turning them in will enrich the idle mix. However, the stock air screws have hollow tips and this effectively limits their adjustment range. Turn them in an eight of a turn at a time and test low speed pick up from about 1500 rpm in gear. Mark your throttle so you know you aren't feeding it more than 1/2 a throttle twist. Keep turning in the screws and testing until no improvement in pick up is obtained, then back them out 1/8 turn to the last best adjustment.
If you still find the throttle response unacceptable, then you will need a larger slow jet. Your bike should have a #38 if stock. You could get a #40 from a cb500, or from motorcyclecarbs.com or sudco.com.
You may have guessed that this idle enrichment may not fix your mid and high speed issues and you are correct. Although, the low speed has some effect on the mid and WOT throttle positions, it's contributions are small. And, the lack a restrictive filter element can have repercussions with both the slide needle setting and the main jet size.
Your main jet should be #100 if it is stock. But, you might not need to change that. You may get by with raising the slide needle another clip position. Test drive and if you still have difficulty getting to top speed with WOT, then you will likely have to go with a larger main jet, as well.
Of course, you can probably avoid all the this test and adjustment by obtaining and installing the stock air box. Even with a Uni Foam filter element inside, all the stock, factory settings, and adjustment, make the bike work well in the street environment.
Cheers,
