I would not include the resistor and LED on the schematic, since they won't be on the board.
I would make a separate mechanical drawing (think AutoCAD, or any cheaper alternative) with the (populated) board, the resistors and LEDS and how to connect them (and how to bend the wires, where to cut them, where to solder etc.
That drawing would also have a BOM associated with them, containing the board, the resistors, the leds and solder.
Such a mechanical drawing is quite common to specify all the non-board things that go into a project. E.g. the casing, mounting material, external components (knobs, connectors, switches) that are not on the board but connected through wires/connectors.
Optionally, I would draw the resistor and led as drawing/illustration on the schematic. That would make it better documented, provided you keep it up to date (i.e. change the resistor details if the resistor changes on the mechanical drawing/BOM.
Theoretically, you could put the resistor and LED on the schematic as unconnected components. That would bring them into the BOM, but would give you PCB design errors, and won't let you document how to connect them.
For a one-off private project, that can be acceptable.