The one at the front, behind the steering head is part of the head steady arrangement. Odd thing to cut off.
The two hooks on the right side top tube are for a tyre pump.
The lugs on the bottom tubes are for the centre stand.
The closed off ends of the seat subframe tubes are the same as my 1957.
I expect the tabs under the seat are for the oil tank and tool box. I haven't got those original parts on mine.