How to resize USER partition:
You will need:
ninfs
linux
~/.switch/prod.keys (with your bis keys) (hint: use lockpick)

First, mount your emuMMC's rawnand as a loop block device:
$ losetup -f --show -o 0x800000 emummc.bin

This will output the location of the block device it just mounted (usually /dev/loop33 for me).

Next: Backup files in USER.
$ mount_nandhac /dev/loop33 ~/mount
$ losetup -f --show ~/mount/USER.img
$ sudo mount /dev/loop34 ~/mount2
$ sudo cp -r ~/mount2/* ~/user_backup/
$ sudo umount ~/mount2
$ losetup -d /dev/loop34
$ sudo umount ~/mount
(Assuming the first losetup output /dev/loop33 and then second output /dev/loop34)

Now: Resize the rawnand gpt's USER entry
$ gdisk /dev/loop33
i > 11
d > 11
n > enter > +XXG/M with XX being whatever size you want and M or G depending if you want it in MebiBytes or GibiBytes > Enter whatever the i > 11 output for "Partition GUID code: ".
c > 11 > USER
x > c > 11 > Enter whatever the i > 11 output for "Partition unique GUID: "
a > 11 > 0 > enter
finally, i > 11 and verify everything matches the original i > 11 apart from last sector and size
w > Y


Finally: Reformat the decrypted USER partition and replace files
$ mount_nandhac /dev/loop33 ~/mount
$ losetup -f --show ~/mount/USER.img
$ gparted /dev/loop34
Reformat as a FAT32 partition and then close this out (It should show that a FAT32 partition already exists, if not you did something  wrong when editing the gpt)
$ sudo mount /dev/loop34 ~/mount2
$ sudo cp -r ~/user_backup/* ~/mount2/
$ sudo umount ~/mount2
$ losetup -d /dev/loop34
$ sudo umount ~/mount
$ losetup -d /dev/loop33

Finally, truncate your emummc image by however much you shrunk USER by, and fix gpt headers:
$ truncate -s -XXG/M emummc.img
$ losetup -f --show -o 0x800000 emummc.bin
$ gdisk /dev/loop33
x > e > w > Y
$ losetup -d /dev/loop33

This should now be complete! Probably a better way of doing some of this, but this is what worked for me