Alright so let's talk about those of so fun microUSB mods shall we?
They looks nice, are functional but can fry your 3DS depending how they are hooked up. So let's take a closer look at what's going on and what we can use to stop the frying parts. You never want to let the magic smoke out or the circuit stops working after all!
The 3DS eMMC uses 3.3V logic which are not 5V tolerant and if you plug a standard microUSB cable with the Vcc tied to any of the eMMC pins into the system it will fry the chip. No magic smoke smell but it doesn't work any more and will forever give you the boot error screen.
If we look at a microUSB port there are 5 connection points total. Vcc, D- , D+, ID, GND. So why don't we try and use D- for CMD, D+ for CLK , ID for DAT0 (or in any way you perfer) and GND so there isn't a chance of 5V on the line if it gets hooked up to a normal USB cable to a computer. The Vcc bus is then hooked to the 3DS power in socket so it can be charged through the port.
Well I did just that and tested it with a couple computers, chargers ("smart" and dumb) ones and so far my N3DS is working just fine. Typical USB host expect the Data lines to be 0 V to 0.8 V for a Low level and 2 V to 3.6 V for a High level. This is within the allowed levels of the eMMC pin tolerances, while many eMMC are 1.8v they also 3.3v logic levels. I will note that the computer could not be used to charge it as it tries to negotiate the speed and power of the connection. The charge light just flashes a bunch, the 3DS says it's encountered and error, and the computer says my USB is malfunctioning, disconcerting and rebooting the 3DS results in it booting just fine.
In practice it's simple, but I did some testing before just deciding to hook up the wires sightly differently lol. At first I used a TXB0108 to force the same logic levels when talking back and forward from the eMMC at 3.0V to 3.3V on the other end hooked up to a computer. During this processes I used an oscilloscope to check the voltage level of both the eMMC and the USB data lines making sure that their outputs were not higher then around 3.6V. The logic conversion was just for safety. For further testing I started shorting the data lines together to simulate what some of the charges do according to the USB charging specs and the 3DS system just returns an error.
Let's discuss some safety considerations, first be careful and to allow better charging compatibility; the USB data lines should be disconnected via physical switch or similar. Another note of importance is the distance between the pins on the USBmicro female connector; they are very close together so if the 5v pin is bent a little it could cause an arc and thus send way more then 5v to the adjacent pin. To remedy this the pins should coated or encapsulated in a non-conductive material. In my case I use an acrylic based conformal coating with high viscosity so I know it gets in between everything. Standard USB cables do not have the ID pin in use or even have a wire connected so that should be just fine.
Though better passive and active components could be added to ensure that if a spike of above 3.6V ever does occur on the USB data lines it will safely and quickly dissipated. Here's a couple quick images of it all, nothing impressive.