4.
I level the tone holes from the INSIDE, like a dent repair. Because metal has memory, the tone holes, even on a new sax, are warped. I gently push the tone holes up at the low spots, working from the inside a little at a time until they are level. The high spots sometimes get a little tapping down. Of course, the tube must be straightened first.
With relacquered saxes, the tone holes probably have been buffed in the relacquering process, leaving tone holes with valleys and peaks wherever the buffer engaged the tone hole chimney. These valleys and peaks may be impossible to remove by the usual methods, so I occasionally have to get out the file. Even with a relacquered horn, files should be used sparingly.
Note: on King and Martin saxes the tone holes are soldered onto the tube. Unless there is damage or sever warping I generally avoid trying to level the tone holes because there's always the danger of breaking the solder. Soldered on tone holes are usually more level than extruded tone holes, anyway.