OK, finished with success ^^
Had to still do a couple small cuts on the pogo board (5th pic) so that the base casing would fit, it has small plastic strips that hug around the analog stick, so i had to make room for those, after that, just a piece of tape is enough to keep the pogo pins in place and close the 3ds easily. And had no need for sponges or rubbers to hold it in place.
Also found out the bad way that u can't pass the wires above the empty area there on the pcb on the right side or they'll get cut by the bottom casing when it's closed.
I made 2 dumps, i made one, then disconnected wiring to the usb card reader, disconnected 3ds, reconnected everything, did another dump and got both dumps with 988 807 168 bytes, md5 match, and "NCDS" at 0x100 so i think i have good dumps.
P.S.: I patented those orange and green temporary case lockers to keep the 3ds shell closed while reading/flashing the nand, so ask for permission 1st if u want to use same method!