EDIT: You (probably) want to face the CPU fans in the opposite direction of my pictures (ie. fan hub towards the heatsink.) This orientation should better match the original inset fans and the original airflow into the middle of the heatsink and out the sides.
I just replaced the fans on my Naomi 2 so I wanted to write it up.

What you need:
CPU:
2x Noctua NF-A4x10 5V 40mm x 10mm fans for the CPUs
8x 3mm x 16mm screws
Case:
1x Gelid Silent 6 FN-SX06-32 12v 60mm x 60mm x 15mm fan
1x 2 Pin Male AMP UP Connector 176271-1
2x Male AMP UP Pins 175151-1
or
splice the old connector with solder/tape/whatever you want.
The case fan is pretty straightforward, but it's 3 wires and they're all black, so you'll need to identify power and ground. Just cut the sense wire short. Power is the middle wire.

(not my pic)
Cut the connector off the new fan and crimp on a new connector or splice on the old connector on, matching ground to black and power to red. I spliced mine since it seems I have everything but 2 pin amp connectors on hand.

The fan fits slightly snug as it's actually 15.5mm thick, but it does fit. Make sure you face the grill part outwards, as that's the way the fan (and generally all fans) blows.

Onto the CPU fans, they're more or less straightforward too.

First you need to repin the connectors. The wire colors match the original fans, but the position doesn't. Basically just swap black and red. It's really easy: press down on the tab on the pin from the side of the connector and it should slide right out. You might need to pry the tab back up if it doesn't lock back into place. The connector will fit just fine on the motherboard headers, but it isn't keyed, so pay attention to the orientation.

The Noctua fan mounting points are smaller than the original fans. Just orient the fan so its more or less centered. Then you can carefully screw the screws into the heatsink. They will thread themselves between the fins and should hold tight and go in nice and straight. Basically just don't be stupid.
Power it on and make sure all the fans spin before you put the case back together. Nothing bad should happen if you got the wires wrong, and afaik it won't boot.
And that's it. Hope this helps.
I just replaced the fans on my Naomi 2 so I wanted to write it up.

What you need:
CPU:
2x Noctua NF-A4x10 5V 40mm x 10mm fans for the CPUs
8x 3mm x 16mm screws
Case:
1x Gelid Silent 6 FN-SX06-32 12v 60mm x 60mm x 15mm fan
1x 2 Pin Male AMP UP Connector 176271-1
2x Male AMP UP Pins 175151-1
or
splice the old connector with solder/tape/whatever you want.
The case fan is pretty straightforward, but it's 3 wires and they're all black, so you'll need to identify power and ground. Just cut the sense wire short. Power is the middle wire.

(not my pic)
Cut the connector off the new fan and crimp on a new connector or splice on the old connector on, matching ground to black and power to red. I spliced mine since it seems I have everything but 2 pin amp connectors on hand.

The fan fits slightly snug as it's actually 15.5mm thick, but it does fit. Make sure you face the grill part outwards, as that's the way the fan (and generally all fans) blows.

Onto the CPU fans, they're more or less straightforward too.

First you need to repin the connectors. The wire colors match the original fans, but the position doesn't. Basically just swap black and red. It's really easy: press down on the tab on the pin from the side of the connector and it should slide right out. You might need to pry the tab back up if it doesn't lock back into place. The connector will fit just fine on the motherboard headers, but it isn't keyed, so pay attention to the orientation.

The Noctua fan mounting points are smaller than the original fans. Just orient the fan so its more or less centered. Then you can carefully screw the screws into the heatsink. They will thread themselves between the fins and should hold tight and go in nice and straight. Basically just don't be stupid.
Power it on and make sure all the fans spin before you put the case back together. Nothing bad should happen if you got the wires wrong, and afaik it won't boot.
And that's it. Hope this helps.
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