if you disconnect the orange from the 3 port valve and it stills fires, as you've stated, its not the control side at fault i.e cylinder stat or room stat. disconnect the switched live at the boiler if it still fires up then you know its a boiler problem probably circuit board or the pump overrun relay has failed and is putting a feed to the switched live as they are internally connected in the boiler. i'd say, if it doesnt fire up then you know its getting a supply via the switched live somewhere via the controls but by the sounds of your description this has been eliminated already, you also shouldnt run this boiler with the main cover as stated before as it is a positive pressure boiler.