I'd turn on each faucet separately and stop, then time the drain. Once you find the slowest drain, you found where the problem is originating around and needs looked at, as that drain is slowing down the flow of other drains working properly of going to the main drain.
I remember once of needing to remove each bathroom sink/tub drain pipe to clean out at the stopper lever bar that goes through the drain pipe of each sink/tub in a split level 2 bath home trying to find a slow drain. Hair especially, catches on everything and plugs up over time when soaps also get involved then buildup over time.
You might also need to go onto roof and see that all air vent pipes are clear by looking down into with flashlight of any wasp nests/bird nest that may of broken up and fallen into pipe and will stop up air flow to different areas of the house drains. You'll have more than one air vent for separate areas like kitchen and bathroom(s).
Get back to us to say what you find. Hope it's simple, but seeing you have a cleared main drain, you got something slowing the air/water flow before reaching the main if everything worked great before.