Hello, tell me what the boiler water pressure is at the boiler, send me a few pictures of the boiler, taken from different sides etc so i can see what the piping issues are.
So far it sounds like there is air in system, and...also that the boiler water pressure is too low to allow water to reach the upper floors, I also need to know the elevation from the boiler to the highest radiator approximately.
This above is only *one of the issues.
The fact that you can get hot water circulation to the upper floor radiators by manually operating the thermostat, refutes my air in the system, low water pressure assumption and makes the issue purely an electrical controls issue.
To that end I need the brand and model number of the thermostat or control that you must set on manual to get heat, some photo's of that wiring will also be useful.
You can use the paper clip icon at the right end of the dialog box tool bar to attach the photo's.
We can go from there.