Issues after upgrade

i upgraded today 18.06.0 to 18.06.1 and am having a few issues now

first off all my packages are gone (after readingthe guide) some more i guess this is to be expected

However i have exroot and my overlay setup on external drives so the upgrade shouldnt have touched them. so i really think i just need to set that back up

i have reinstalled some packages and now have my usb back to being mounted how they were before with one exception, my overlay isnt mounted right:

free%20space%20for%20software mount%20info

Current /etc/config/fstab

config global
        option anon_swap '0'
        option anon_mount '0'
        option auto_swap '1'
        option auto_mount '1'
        option delay_root '5'
        option check_fs '0'

config swap
        option device '/dev/sda2'
        option enabled '1'

config mount
        option fstype 'ext4'
        option enabled '1'
        option auto_mount '1'
        option options 'rw'
        option enabled_fsck '1'
        option device '/dev/sda1'
        option target '/mnt/usb1'

config mount
        option  target  '/overlay'
        option  device '/dev/sda3'
        option  fstype  'ext4'
        option  enabled '1'


config mount
        option fstype 'ext4'
        option enabled '1'
        option auto_mount '1'
        option options 'rw'
        option enabled_fsck '1'
        option device '/dev/sda1'
        option target '/mnt/usb1'

config mount
        option fstype 'ext4'
        option enabled '1'
        option auto_mount '1'
        option options 'rw'
        option enabled_fsck '1'
        option device '/dev/sdb1'
        option target '/mnt/usb2'

FYI
I did forget to create a backup before upgrading. Mostly because i backup the /etc folder every night but now i'm seeing that isn't enough. I did restore my backed up /etc folder however that did not fix the issues mentioned above
i have another backup from August (there shouldn't be many changes after this point) that i created via luci, but i have restored that and it also did not fix anything.

This will return a list of installed packages and dependencies.
(make sure ext-root is mounted)
find /overlay -iname '*.list'

i dont understand. if you look at the luci screen shot and mount command results below, they show
/dev/ubi0_1 /overlay
but it also shows in the mount point section
/dev/sda3 (10513 MB) /overlay

also if you look at my fstab (posted above) it should be /dev/sda3 , idk what is assigning this /dev/ubi0_1 to overlay ?

Results from mount:

root@Skittles:~# mount
/dev/root on /rom type squashfs (ro,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,noatime)
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,noatime)
tmpfs on /tmp type tmpfs (rw,nosuid,nodev,noatime)
/dev/ubi0_1 on /overlay type ubifs (rw,noatime,ubi=0,vol=1)
overlayfs:/overlay on / type overlay (rw,noatime,lowerdir=/,upperdir=/overlay/upper,workdir=/overlay/work)
ubi1:syscfg on /tmp/syscfg type ubifs (rw,relatime,ubi=1,vol=0)
tmpfs on /dev type tmpfs (rw,nosuid,relatime,size=512k,mode=755)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,mode=600,ptmxmode=000)
debugfs on /sys/kernel/debug type debugfs (rw,noatime)
/dev/sdb1 on /mnt/usb2 type ext4 (rw,relatime,data=ordered)
/dev/sda1 on /mnt/usb1 type ext4 (rw,relatime,data=ordered)

Results from command:

root@Skittles:~# find /overlay -iname '*.list'
/overlay/upper/usr/lib/opkg/info/libmbedtls.list
/overlay/upper/usr/lib/opkg/info/kmod-usb-ehci.list
/overlay/upper/usr/lib/opkg/info/e2fsprogs.list
/overlay/upper/usr/lib/opkg/info/kmod-fs-ext4.list
/overlay/upper/usr/lib/opkg/info/libsqlite3.list
/overlay/upper/usr/lib/opkg/info/libblkid.list
/overlay/upper/usr/lib/opkg/info/libflac.list
/overlay/upper/usr/lib/opkg/info/block-mount.list
/overlay/upper/usr/lib/opkg/info/libuuid.list
/overlay/upper/usr/lib/opkg/info/libbz2.list
/overlay/upper/usr/lib/opkg/info/libvorbis.list
/overlay/upper/usr/lib/opkg/info/libss.list
/overlay/upper/usr/lib/opkg/info/kmod-scsi-core.list
/overlay/upper/usr/lib/opkg/info/libcomerr.list
/overlay/upper/usr/lib/opkg/info/samba36-server.list
/overlay/upper/usr/lib/opkg/info/minidlna.list
/overlay/upper/usr/lib/opkg/info/kmod-lib-crc16.list
/overlay/upper/usr/lib/opkg/info/ca-bundle.list
/overlay/upper/usr/lib/opkg/info/libcurl.list
/overlay/upper/usr/lib/opkg/info/libevent2.list
/overlay/upper/usr/lib/opkg/info/luci-app-samba.list
/overlay/upper/usr/lib/opkg/info/librt.list
/overlay/upper/usr/lib/opkg/info/libjpeg.list
/overlay/upper/usr/lib/opkg/info/kmod-nls-base.list
/overlay/upper/usr/lib/opkg/info/libexif.list
/overlay/upper/usr/lib/opkg/info/libopenssl.list
/overlay/upper/usr/lib/opkg/info/kmod-usb-core.list
/overlay/upper/usr/lib/opkg/info/libnatpmp.list
/overlay/upper/usr/lib/opkg/info/kmod-crypto-crc32c.list
/overlay/upper/usr/lib/opkg/info/transmission-daemon-openssl.list
/overlay/upper/usr/lib/opkg/info/kmod-crypto-hash.list
/overlay/upper/usr/lib/opkg/info/libext2fs.list
/overlay/upper/usr/lib/opkg/info/libid3tag.list
/overlay/upper/usr/lib/opkg/info/libffmpeg-mini.list
/overlay/upper/usr/lib/opkg/info/luci-app-minidlna.list
/overlay/upper/usr/lib/opkg/info/kmod-usb-storage.list
/overlay/upper/usr/lib/opkg/info/libminiupnpc.list
/overlay/upper/usr/lib/opkg/info/luci-app-transmission.list
/overlay/upper/usr/lib/opkg/info/kmod-usb2.list
/overlay/upper/usr/lib/opkg/info/libogg.list
/overlay/upper/usr/lib/opkg/info/zlib.list
/overlay/upper/usr/lib/opkg/info/kmod-usb3.list