Introduction
The motherboard should only be replaced as a last resort. Be careful removing it!
What you need
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Fully power off the console and flip it upside down.
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Remove the game card, headphones, charging cable, stylus, and anything else connected.
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Use a JIS 0 screwdriver to loosen the two black captive screws on the back cover.
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Remove the MicroSD card by pressing it in with your thumbnail until it clicks and partially ejects, then pull it out.
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Using a JIS #00 screwdriver, remove the six 6mm screws around the edges of the secondary cover.
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Use the flat end of a spudger to disconnect the shoulder button cable press connectors.
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Remove the back cover.
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Use tweezers to flip up the small, hinged locking flap in order to unlock the ZIF connector securing the Circle Pad ribbon.
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Slide the ribbon out of the ZIF connector.
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Using tweezers, gently pull the four marked ribbons out of the ZIF connectors along the sides of the motherboard.
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Three of the ribbon connectors have plastic clamping flaps that cover the ribbon to prevent slippage. Use the tweezers to flip them up before ribbon removal.
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This one ribbon connector may also have a plastic clamping flap, but it's not like the others, rather it's similar to the one used for the Circle Pad. Gently flip up the flap on the side opposite the ribbon cable to remove the cable.
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Carefully pivot the motherboard 90 degrees toward the hinges to reveal two more ZIF connectors on the underside of the motherboard.
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Both have latches that must be flipped up. The left, longer latch is black; the right, shorter one is white. Flip up the flaps, slide the ribbons out and remove the motherboard.
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To reassemble your device, follow these instructions in reverse order.
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13 Guide Comments
With some digging, I managed to find this on the GBAtemp forums , which host a community of 3DS modders:
https://gbatemp.net/threads/screwed-up-p...
Seems like no one's quite sure, but it could be a start. Unfortunately, the N3DS components are largely small black boxes with no labeling.
If you have a multimeter, it might help to test some of these mystery boxes.
Question: Seeing as how you pulled the red cable in the photos, how was that fixed? Asking for a friend.
We...never fixed that actually, as we didn't have the tools for it and the device had been loaned to us specifically for tearing down.
I don't know if iFixit themselves ever did anything with it, but I would imagine soldering the frayed end of the cable back onto the plug would work. (Here's a guide on that: http://www.instructables.com/id/Solderin... )