Is your check engine light still on? If you still have a faulty EGR valve, it generally gets stuck open and floods the engine with exhaust gas which will soot up the turbo actuator as well as flooding your DPF downstream. While it is technically possible to replace just the actuator, it's not likely that you will find someone to do it if you can't do it yourself and you will probably end up needing a new turbo. Not to say it's impossible, but most shops aren't going to want to mess with it.

The turbo code you probably got was p2262 boost not detected which is mechanical failure of the actuator to move through it's range of motion test when you start the truck. When the actuator gets screwed, it can cause a variety of issues from the exhaust brake not working to the brake getting stuck on while driving to inability to make boost. Any of these can be attributed to how the truck has acted in your description at various times and it will often "go back to normal" after shutting the truck off only to act up again when it gets stuck again later.

In any event, your air filter is not going to be the source of the problem. Do not remove it and run the truck.