This is not shown well - but to separate the top part of the 3DS from the bottom (sorta as shown in step 21 but not done in step 18) - refer to step 18's picture of the circuitry, LCD, and speakers. Be careful, damaging a cable here = potentially dead 3DS.
First, the 3 ribbon cables from step 11 must fed through a plastic slot in the bottom part (where the cutouts of the d-pad + buttons are), then GENTLY coiled sideways like an ice cream cone through small hollow silver cylinder (that's narrower than the cables are wide) and through a cylinder on the top part (where the non-touchscreen is), pictured in step 18 near where the brown/black ribbon cables intersect.
On the opposite side, left of the notification LED, there is a removable silver dowel (solid cylinder). With a T-pin (or a sturdy needle), pry the dowel to the left, "toward" the LCD. There is a little notch on the dowel that will help. Once the dowel is fully to the left, the two halves of the 3DS can be separated, and the dowel removed.
Disclaimer: I replaced my front panel entirely, and threw away the old one.
If you do not have a replacement front panel, gently removing it (without getting the adhesive oily from your fingers/dusty) and replacing it is an option. The adhesive is incredibly tacky, and while removing the front panel will weaken the adhesive - it will likely be sticky enough to do its job. If not, double-sided tape or small amounts of water based craft glue may help (disclaimer again: I haven't tried these)- do NOT use superglues/liquid cements/epoxies.
#00 will work - but you must press down firmly and sort of jerk the screw out a few degrees at a time. If you don't press firmly, the screws strip very easily. Using #000 will strip the screws more easily.
Once the motherboard is out, all the buttons and button membranes in the bottom part of the plastic shell are free to move. Turning or jostling the shell will result in a lot of plastic pieces everywhere.
Removing the cables must come after step 13 (step 12 if you fudge things) - but the pictures in step 11 are better suited to showing cable order.
The guide skims over this part - though it's one of the most important.
The speaker ribbon cable (first picture, lower left, topmost cable/smallest of the 3 ribbons in this area) connects to the mobo goldteeth facing away from keyboard (damage/improper assembly will result in a non-bootable 3ds that has the power LED flash for less than a second before turning off). The white line shows where a fold should be.
The camera cable (directly underneath speaker cable, largest of the 3 ribbon cables) connects with goldteeth facing the mobo.
The top LCD (non-touchscreen) cable (opposite side of mobo, medium in width) connects with goldteeth away from mobo. This should be the last cable removed in disassembly, and the first reattached.
If you plan on removing the top part of the 3ds, note of how the 3 cables are oriented (what direction goldteeth face) and layered (which cable is on top of which cable). Doing this incorrectly will likely result in cables not reaching where they need to go (see step 18).
While you can replace the same front panel if you're careful, it will likely be bent (and a small eyesore) from the force required to remove it.
All the screws here mount the mobo to the case. And even though you can remove the mobo with the circle pad ribboned in, the cable may break as it flops around if you're not careful.
These screws strip INCREDIBLY easily. PH00 works, but you need to press down fairly hard and sorta jerk the screwdriver around a few degrees at a time. Even after working this out (by stripping the first one) I accidentally stripped the next-to-last screw I was removing, requiring me to cut the screw well.
Speaker's on the mobo and fairly exposed to water damage if it so occurs - other than cleaning the goldfingers/contact pads and tightening the ~6 screws on the upper plastic shield (the plastic shield is required to be in-place for sound to work), you might be out of luck.