You have to do some research first if the switch you have is the issue. The reason I asked you to experiment without it. If the switch is the issue confirmed then research what people with AiMesh are using when a switch is needed between the Main and Nodes.
I have read that running the nodes in AP mode is much better then using them in mesh, but when using them in mesh i have can use AiProtect and parental controls. Will I loose that when running nodes in AP?
The so called "nodes" are in fact Access Points when wired and Repeaters when wireless. What you'll lose is the limited AiMesh "central management" and Guest Network to "nodes" propagation. Everything else on the main router will remain the same and functional.
Home "mesh" marketing invented "nodes, satellites, pods" and "wired backhaul" terms.
I finally ditched the AiMesh and made the "Nodes" to true AP. Set the same SSID for everything and different channels for each one. Works much better. I get much better signal and the roaming is more or less seamless. And parental controls work.
Clients are still a bit sticky, so either adjust with roaming assist or adjust TX-rate?
Parental Controls is unrelated to AP function. You can try both Roaming Assistant and Power adjustments for better roaming. With only 2x APs and tri-band you can use the same channels on both. Available bandwidth on 3x radios will be high enough for home environment.
I have a router in the basement and 2x AP:s, one on each floor. I have set different channels on all three of them. Should I have same channel for the 2x AP:s while having the router itself on a different channel?
Experiment and see what works better for you. Everyone has different Wi-Fi environment with different number of devices with different requirements. There is no universal best advice. I run a few multi-AP systems and they are all set differently according to location specifics.