1. To NOT use the A/B mod, simply install your D1-D4 diodes directly on the board.
2. To use the A/B mod, you need to add an external DPDT switch. This switch is best used with one of Barry’s DPDT wiring boards (temporarily out of stock). The switch is wired to the A and B pads and different diode pairs are wired on either side of the DPDT switch. A useful photo will be available when these switch boards are back in stock. When using this mod, you do not install any diodes on the main board in positions D1-D4.
The extra solder points that you mention are there to facilitate installing either a LED or a axial diode depending on the component’s lead spacing. You would only use 2 of the three in each position.