Pinouts

CTR CPU B

G	0?	CS1	?	?	D5	D2		RST	CLK	G	G	X	X	3v3	3v3		3v3					?	?	?		IRIRQ	?	?	G
1?	2?	CSx	CSy	?	D6	D3	D0	IRQ	CS1	G	G	G	G	3v3		3v3		G			?	?	?	?				?	?
3?																												?	?
			3v3		D7	D4	D1	DET	CS2	G	G	G	3v3		3v3	G	3v3	3v3	3v3	?	?	?	?	?	IRTX	?		?	?
CLK	D0			G	1v2	3v3	G	1v2	3v3	G	1v2	G	G	1v2	3v3	G	1v2	3v3	G	1v2	3v3	G	1v2	3v3	G	?		?	?
D1	D2		D3	3v3																					1v2	?		?	?
CMD	IRQ		WP	1v2																					1v8	?		?	?
CLK	D0			G			3v3	G	3v3	G	1v2	G	3v3	G	1v2	G	3v3	G	1v2	G	3v3	G			G	?		?	?
D1	D2		D3	3v3			G	3v3	G	3v3	G	3v3	G	3v3	G	3v3	G	3v3	G	3v3	G	1v2			1v2	?		?	?
	CMD			1v2			1v2	G													1v2	G			1v8	?		?	?
?	?		?	G			G	3v3													G	1v8			G	?		?	?
	?		?	3v3			3v3	G													1v2	G			1v2	?		?	?
				1v2			G	3v3													G	1v8			1v8	?		?	?
				G			1v2	G													1v8	G			G	?		?	?
SCL				3v3			G	3v3													G	1v2			1v2	?		?	?
SDA				1v2			3v3	G													1v8	G			1v8	?		?	?
	?		?	G			G	1v2													G	1v8			G	?		?
?	?		?	1v8			1v2	G													1v8	G			1v2	?		?
?	?		?	1v2			G	1v8													G	1v2			1v8	?		?	?
?	?		?	G			1v8	G													1v8	G			G	?		?	?
?	?		?	1v8			G	1v8													G	1v8			1v2	?		?	?
G	?		?	1v2			1v2	G	1v8	G	1v8	G	1v8	G	1v2	G	1v8	G	1v8	G	1v8	G			1v8	?		?	?
?	?		?	G			G	1v8	G	1v2	G	1v8	G	1v2	G	1v8	G	1v2	G	1v8	G	1v2			G	?		?	?
?	?		?	1v8																					1v2	?		?	?
?	?		?	1v2																					1v8	?		?	?
?	?		?	G	1v8	1v2	G	1v8	1v2	G	1v8	1v2	G	1v8	1v2	G	1v8	1v2	G	1v8	1v2	G	1v8	1v2	G	?		?	?
?	?		?	?	?	?	?	?	?	?	3?	4?	5?					B	PADR	PADD	G	?	?	G	?	?		?	?
?	?																											?	?
G	G	?	?	?	?		?	?	?	?	SDA	1?	2?					A	STRT	PADU	L	Y	?	?	?	?	?	?	?
G	?	?		?	?	?		?	?	?	SCL	0?							SLCT	PADL	R	X	?	?	?	?	?	?	G

legend:

SoC clock crystal
RTC clock crystal
Gamecard
SDCARD SDIO
NAND SDIO
WIFI SDIO
SPI
I2C-1
I2C-2
I2C-3
Pad
FCRAM
Camera
WIFI
GPIO
LCD0 (small)
LCD1 (big)
CODEC0 (unknown)
CODEC1 (unknown)
MCU (unknown)
POWER
Ground

Orientation: Triangle bottom right on the PCB.

UC CTR

The MCU seems to most closely resemble an NEC (Renesas) 78K0R/Kx3-L 64-pin FBGA: https://www.renesas.com/us/en/document/mah/78k0rkx3-l-users-manual-hardware-r01uh0106ej040078k0rkx3l?language=en&r=1051991

The functional pin mapping is almost exactly the same, except the GPIO port assignment is almost completely different.

Most low port numbers appear to map to the correct physical pin locations as described in the above datasheet, however around P7 and above this mapping is definitely altered.

Orientation: Pin 1 marker in bottom left corner

Pinout

/	A	B	C	D	E	F	G	H
8	+	G			TP75	X	X	?
7	SCL		G		/RESET	?	?	+
6	SDA		+	TP77	TP76			+
5	?		TP78	PWRLED1				CHRGLED
4							G	G
3		PWRBTN					BATTTHM
2				PWRLED0			HOMEBTN
1	+				SCL	SDA		G

Pin assignment

und = undocumented / custom
SFR = Special Function Register (SFR bank 1, range FFF00h - FFFFFh)
ESR = Extended Special Function Register (SFR bank 2, range F0000h - F0806h)
/   = active low (ground to enable, pull to power supply to disable)

TP	Pin	Port	Purpose
TP79	A8	EVdd	Digital voltage source input (positive)
TP74	E7	/RESET	Resets the MCU when grounded, but is also used when reprogramming
TP75	E8	FLMD0	Flash mode(?) used when reprogramming with external programmer
TP76	E6	TOOL1	Used when using an ICE or debugger
TP77	D6	TOOL0	Multipurpose pin for reprogramming and debugging
	A7	SCL0 / P6.0	DSi-side I2C SCL
	A6	SDA0 / P6.1	DSi-side I2C SDA
	E1	SCL1 / ESR[510h].und	3DS-side SCL
	F1	SDA1 / ESR[510h].und	3DS-side SDA
	F7	/P0.1	SocReset_n (one of the two SoC reset signals)
	G7	/P0.0	SocReset_n (one of the two SoC reset signals)
		/P3.0	Unknown. Probably resets something, as it's poked in a similar pattern to the SoC reset signals.
		P5.0	Toggles something (poked in conjunction with reset signals)
		P2.0	HOME button
		P4.3	Charging LED(?)
		P5.1	Charger "button"
		P7.0	???
		P2.4	BatteryChargeState (?)
		P7.3	Power button
		P7.4	WiFi button
		P7.6	External IRQ (MCU --> SoC)

CODEC

	4?	3v3		3?	0?	?	?		G
	3?	5?	G		1?	CSx	?		G
G	2?	0?	G		2?	CSy				SPEAKER1
TOUCH	TOUCH	1?	G	G	G	G	G	G		SPEAKER1
TOUCH	TOUCH		G	G	G	G	G	G
CPAD	CPAD		G	G	G	G	G	G
			G	G	G	G	G	G		SPEAKER2
MIC		G	G	G	G	G	G	G		SPEAKER2
JACK_R	G	G		G						G
3v3				G	G	G	G
		G				JACK_L		G	G

LCD (old3DS bottom)

Pin number	Name	Description
01	-6V
02	12V
03	CLK	Pixel clock
04	/HBL	Horizontal blank (low while blanking)
05	/VBL	Vertical blank (low while blanking)
06	2v2	Loopback of pin 07?
07	2v2	Content latch? Shorting this to ground or to pin 06 will "lock" the screen memory while still allowing the screen to refresh itself.
08	GND	"chassi" ground
09	HCL	Horizontal clock
10	GND	"chassi" ground
11	BIAS 1	Default ~ 4.5V - 4.8V; sets contrast
12	BIAS 2	Usually matches BIAS 1; sets "flicker"
13	???	Might be a transistor? Shorted to ground if off, 2.36V if on.
14	6V
15	???	Loopback of pin 14 ? Shorting this with pin 14 or ground will make the 3DS turn off with a harsh pop sound.
16	???	???
17	???	???
18 [...] 25	RED 0 [...] RED 7	Red pixel bits
26	GND	"chassi" ground
27 [...] 34	BLUE 7 [...] BLUE 0	Blue pixel bits
35	GND	"chassi" ground
36 [...] 43	GREEN 7 [...] GREEN 0	Green pixel bits