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You can easily make your own ‘power LED’.
I’m thinking of turning off the on-board LED by desoldering R48 completely.

Your own ‘power LED’ can then be connected to 12V from the Molex connector to get the exact same function as the on-board LED – OR – you could use the power from the GPIO headers to indicate that the 3V3 or 5V buck converters are actually doing their jobs properly.

To do this …
For 12V I recommend using a 4K7 … 10K resistor; this will make sure your LED does not use a lot of power and that it won’t blind you.
For 5V and 3V3, I recommend a 1K resistor; this usually gives a pleasant light and will use very little power (3.3mA or 5mA).

-Connect the resistor in series with the LED on the Cathode side. Connect the other end of the resistor to pin 1 or pin 2 of GPIO header J17.
For 3V3, connect the Anode of the LED to either pin 3 or pin 4 of GPIO header J17.
For 5V, connect the Anode of the LED to either pin 5, 6, 7 or pin 8 of GPIO header J17.
Alternatively, for 5V, you could instead connect the Anode of the LED to pin 4 of the Molex connector and the resistor to pin 3.
For 12V, connect the Anode of the LED to pin 1 of the Molex connector and the resitor to pin 2 of the Molex header.

For details on 3V3 and 5V, see page 4 of the schematic.
For details on 12V, see page 12 of the schematic (lower left corner).

As for the “harddisk light”, this might be more tricky than you’d expect.
These days, harddisks do not support external LED lights.
Some people have successfully found the right signal on their harddisks, hooked into that and amplfied it via a transistor to drive a LED.

-But there might be an alternative. If you’re going to use a cheap port multiplier or a RAID card, there might be header pins for LEDs, which you can easily connect to via dupont connectors. Same rule as for the power LED: use a 1K resistor for 3V3 to 5V, then you won’t get a too bright light (if you want a brighter light, you can use resistors down to 270 Ohm with most LEDs, but I’d recommend staying above 470 Ohm).

I know that the cheap JMB321 port multiplier from IOCrest / StarTech / Syba / Addonics / whateverelsetheycallthemselves, that you can get on eBay and Amazon has an activity LED, which you can hook into.
This port multiplier uses only 250mA and needs 5V for power. Unfortunately, it’ll limit your throughput to 3Gbits, so your 6Gbit SATA drive won’t be as fast if going through that PM.

If you want a faster port multiplier, you can get one which is 6Gbit for around 4 times as much; the name of the chip is JMB575.
I do not know if the JMB575 board has an activity LED, though. Make sure it has one, before you purchase. 😉