Help!!! Dirt in tubing and coffee. And which parts need replacement?

I bought a used Gaggia Classic V1 (my first espresso machine, new to espresso). The previous owner had replaced the boiler and gasket before selling and are new. However it was kept in basement during and after repairs. There was dirt inside the housing which got in the water basket and is now in the tubing. How can I get rid of the dirt? I cleaned the machine from the inside, but there is still some dirt coming out. Here are some pictures. Will running the water as long as its not clean in the mug help, or I need to do or use something else?

Also should I replace the group head, screen, and the tubes? I cleaned them as much as I could. Pictures