So after testing out a couple different configurations, card readers and various pins this has been the pinout that works (not just for me anymore!
)
There may be other motherboards as time goes on that look different, so please check before you do anything. Also this is for educational purposes only and you do so at your own risk. It's taken me a couple hours to get it down but I hope it works for you as well to keep your SysNAND backed up manually or you need to restore an image because it somehow got accidentally updated
.
This is for the N3DS XL, just a note but the mobo has the lettering RED-CPU-01.
This is an alternate location on the other side of the board for CLK, it's a test point so it's a large pad to solder to and easier to access.

A ground point that's easy enough to access on the reverse side. There are a lot of them as the board uses a ground pour so you can easily hunt around for one.

Do not use this area (the RED selected area) for a GND point because of the object in blue.

This is for the N3DS (nonXL), just a note but the mobo has the lettering KTR-CPU-01.
This is an alternate test point on the other side of the board for CLK for the N3DS.

If you are on Windows here is a small guide for backing up the system eMMC using Win32DiskImager.
Using the TekRepublic TUC-300 Reader I was still hitting around 6MB/s with just one DAT line and 21MB/s using all the DAT lines. Please let me know of any error or problems in any of my diagrams, this was fun to figure out. I'll keep you updated
Alright so I've tested it fully (backups and writes) with many systems now of, both of my own and other members here, I can safely say this works well with both the Samsung and Toshiba eMMC.
I updated to 9.5 and then restored my backup of 9.0. I posted a couple images on Page 3 post #60.
Please note the N3DS eMMC does not work in every card reader, it can be hit or miss and this list is not exact but these are known to work with the 3DS and N3DS.
For working card readers I have had good success with the:
Anker® USB 3.0 (68UNMCRD-B2U) : Realtek RTS5306
TekRepublic TUC-300 : Realtek RTS5307
Some other card readers that use the same chipset /controller but have not been tested although should work:
Plugable USB3-FLASH3 -
SIIG JU-MR0E12-S1-
Startech FCREADMICRO3 -
Other card readers that work
SanDisk SDDR-121-A11M (older version Grey) : GL827
Transcend P8 TS-RDP8K : ALCOR AU6476 (Thank you Gamerquest1 and zchtoy)
Anker® USB 3.0 4-Slot Card Reader (A7612) : RT5301 (Ava)
Card reader chipsets known not to work on N3DS with the Samsung eMMC, but may still work on one with the Toshiba and the 3DS/XL eMMC:
GL3220
GL3233
GL834
If anyone has any other card readers they have used with success on both the N3DS Toshiba and Samsung eMMC please let me know so I can add them to the list. Thank you!
A little bit more about the card readers I have tested and what works and what doesn't!
So that's the card readers I have and the information I have on them currently. Feel free to chime in with what works for you and what doesn't. As the N3DS eMMC seems to be pickier but not all controllers are made equally and who knows how the firmware on them is. I will add more about them and info
Side Note: Not exactly sure but SIIG, StarTek, and Plugable all make card readers that look just like the TekRepublic one.
Size info for the eMMC's
Samsung 1.21 GB (1,300,234,240 bytes)
Toshiba = 1.84 GB (1,979,711,488 bytes)
A possible way to check if your eMMC image was any good is to look at it with a Hex Editor, I am sure there are better methods though, but this has worked for me. Also as others have said, booting the dump in emuNAND is a good way to check its validity.

Thank you for taking the time to check this out and if you have any questions or comments please ask, I'll do my best to help!
-----------------------------------------------------------------------------------------------------------------------------------
There may be other motherboards as time goes on that look different, so please check before you do anything. Also this is for educational purposes only and you do so at your own risk. It's taken me a couple hours to get it down but I hope it works for you as well to keep your SysNAND backed up manually or you need to restore an image because it somehow got accidentally updated
This is for the N3DS XL, just a note but the mobo has the lettering RED-CPU-01.
This is an alternate location on the other side of the board for CLK, it's a test point so it's a large pad to solder to and easier to access.

A ground point that's easy enough to access on the reverse side. There are a lot of them as the board uses a ground pour so you can easily hunt around for one.

Do not use this area (the RED selected area) for a GND point because of the object in blue.

You can't use the ground near the power connector or on it unfortunately 
If you check around it, it actually goes though an inductor, or transformer, but I am voting it's being used an inductor, before getting to the ground plane. That adds a little resistance to it and I don't think the inductor is charging since there is no power at the connector.
Inductors start off as a open circuit until their magnetic fields are charged and stabilized which then it acts as a short. The reason for the inductor is to help handle changes in current, since the wall supply is a switching supply the inductor here helps stabilize the switching noise from the charger.
P.S. if you have a good multimeter you can check the resistance of the inductor from other points on the GND plane and there should be a bit of difference.
If you check around it, it actually goes though an inductor, or transformer, but I am voting it's being used an inductor, before getting to the ground plane. That adds a little resistance to it and I don't think the inductor is charging since there is no power at the connector.
Inductors start off as a open circuit until their magnetic fields are charged and stabilized which then it acts as a short. The reason for the inductor is to help handle changes in current, since the wall supply is a switching supply the inductor here helps stabilize the switching noise from the charger.
P.S. if you have a good multimeter you can check the resistance of the inductor from other points on the GND plane and there should be a bit of difference.
This is an alternate test point on the other side of the board for CLK for the N3DS.

If you are on Windows here is a small guide for backing up the system eMMC using Win32DiskImager.
Using the TekRepublic TUC-300 Reader I was still hitting around 6MB/s with just one DAT line and 21MB/s using all the DAT lines. Please let me know of any error or problems in any of my diagrams, this was fun to figure out. I'll keep you updated
Alright so I've tested it fully (backups and writes) with many systems now of, both of my own and other members here, I can safely say this works well with both the Samsung and Toshiba eMMC.
I updated to 9.5 and then restored my backup of 9.0. I posted a couple images on Page 3 post #60.
Please note the N3DS eMMC does not work in every card reader, it can be hit or miss and this list is not exact but these are known to work with the 3DS and N3DS.
For working card readers I have had good success with the:
Anker® USB 3.0 (68UNMCRD-B2U) : Realtek RTS5306
TekRepublic TUC-300 : Realtek RTS5307
Some other card readers that use the same chipset /controller but have not been tested although should work:
Plugable USB3-FLASH3 -
SIIG JU-MR0E12-S1-
Startech FCREADMICRO3 -
Other card readers that work
SanDisk SDDR-121-A11M (older version Grey) : GL827
Transcend P8 TS-RDP8K : ALCOR AU6476 (Thank you Gamerquest1 and zchtoy)
Anker® USB 3.0 4-Slot Card Reader (A7612) : RT5301 (Ava)
Card reader chipsets known not to work on N3DS with the Samsung eMMC, but may still work on one with the Toshiba and the 3DS/XL eMMC:
GL3220
GL3233
GL834
If anyone has any other card readers they have used with success on both the N3DS Toshiba and Samsung eMMC please let me know so I can add them to the list. Thank you!
A little bit more about the card readers I have tested and what works and what doesn't!
Okay so here are the card reader controller, makes well enough sense why the Tek-Republic and Anker ones work as they use basically Identical controllers. I wonder what my old Transend TS-RDP5K used to use. Can't find much about the Realtek controllers unfortunately but there are a couple other ones out there that use it from what I have seen. I will be updating as I get / test more that I have access to, also will be adding info from USBDeview v2.41 about each card reader.
Anker® USB 3.0 (68UNMCRD-B2U) : Realtek RTS5306 : Works as decently as the Tek one does, no issues at all on reading or writing
TekRepublic TUC-300 :Realtek RTS5307 : Works well for me on the 3DS/XL and N3DSXL, my go to reader.
Anker® USB 3.0 4-Slot Card Reader (A7612) : RT5301 :Works well for me on the 3DS/XL and N3DSXL
Transcend TS-RDP5K : GL834 Product Info : Sadly I can't get this new one to work for the N3DSXL but still works fine on my 3DS XL
Transcend TS-RDF5K (USB 3.0) : GL3233 Product Info : Same story as above
SanDisk SDDR-121-A11M (older version Grey) : GL827 Datasheet : I've played around with this did some reads and writes to the 3DS/XL and N3DSXL works but it's a microSD reader, hard to use without an adapter or soldering directly to it.
Anker® USB 3.0 (68UNMCRD-B2U) : Realtek RTS5306 : Works as decently as the Tek one does, no issues at all on reading or writing
Side Note: Not exactly sure but SIIG, StarTek, and Plugable all make card readers that look just like the TekRepublic one.
Size info for the eMMC's
Samsung 1.21 GB (1,300,234,240 bytes)
Toshiba = 1.84 GB (1,979,711,488 bytes)
A possible way to check if your eMMC image was any good is to look at it with a Hex Editor, I am sure there are better methods though, but this has worked for me. Also as others have said, booting the dump in emuNAND is a good way to check its validity.

Thank you for taking the time to check this out and if you have any questions or comments please ask, I'll do my best to help!
-----------------------------------------------------------------------------------------------------------------------------------
So I know I posted this in a different thread but I decided I would make a new thread for any input and keeping a record about anything I or someone else figures out.
I've tested the 12 pins around the eMMC both front and back also, the US black N3DS XL I have doesn't use a Samsung eMMC. If anyone knows something about eMMC logic that would be great please get in touch with me.
So I'm pretty sure I've found the DAT 0/1/2/3, as they were pretty obvious just don't know which is which and a couple lines that are definitely clocks. There is a small spike in one of the lines during the clock start up and I wonder if it's the CMD but again i don't have much knowledge on eMMC logic.
I am thinking I am going to utilize my old 3DS and look at that data to give me an idea what each line should look like on system boot up.
It's not very hard to get the N3DS XL into everyone's favorite blue screen of error, hehe.
Also some pretty pictures
PS. - Please ignore the Data part on the top I was playing around with protocol analyzers. Also sorry about the tiny letter and messed up order in the logic analyzer windows.


This is the the pin testing points that I originally used:

I've tested the 12 pins around the eMMC both front and back also, the US black N3DS XL I have doesn't use a Samsung eMMC. If anyone knows something about eMMC logic that would be great please get in touch with me.
So I'm pretty sure I've found the DAT 0/1/2/3, as they were pretty obvious just don't know which is which and a couple lines that are definitely clocks. There is a small spike in one of the lines during the clock start up and I wonder if it's the CMD but again i don't have much knowledge on eMMC logic.
I am thinking I am going to utilize my old 3DS and look at that data to give me an idea what each line should look like on system boot up.
It's not very hard to get the N3DS XL into everyone's favorite blue screen of error, hehe.
Also some pretty pictures
PS. - Please ignore the Data part on the top I was playing around with protocol analyzers. Also sorry about the tiny letter and messed up order in the logic analyzer windows.





This is the the pin testing points that I originally used:

Last edited by Avalynn,