[Nexus 7 Q&A, Help & Troubleshooting] ziffius:
Hi and thanks to anyone who decides to help me as my knowledge is limited.

I decided to flash KitKat as I play a WebView based game and thought the WebView Chromium of KitKat might make it run faster as it ran pretty slow. On the Paranoid Google+ page it says you need TWP 2.6 later and other sites say 2.6.x. I had 2.6.0.0, so did a backup of boot, data, system and recovery using TWRP, copied them to a PC and then tried installing KitKat, it failed. So I updated to TWRP 2.6.3.0 and it failed again, tried a second time and it updated

The game didn't work well on KitKat, so I restored my original version. I then decided to take screenshot of game not working on KitKat to complain, so tried installing KitKat again forgetting to update to 2.6.3.0 as the restoration of the backup restored the prevous 2.6.0.0 recovery, was a noob and tried again and i'm now left with a Nexus 7 in a boot logo loop.

Restoring the backup fails, as does installing the KitKat Zip or Opensensation . If I try flashing TWRP 2.6.3.0 via fastboot, it says success, but when I reboot the recovery i'm still in 2.6.0.0. I can boot into 2.6.3.0 using "fastboot boot", but it still won't restore the backup or flash. I also have a backup of the OpenSensation rom (wanted to try PDroid and it was the only rom I could find prepatched) which I made on 2.6.3.0, that won't restore either.

The error i'm getting in TWRP is "symlink: some failed"", "can't open destination log file: '/cache/recovery/log'" and "E:Unable to open '/cache/recovery/log'"

This is the end part of recovery.log in tmp

E:TWFunc::Copy_Log -- Can't open destination log file: '/cache/recovery/log'
I:Copying file /cache/recovery/log to /cache/recovery/last_log
I:Attempt to load settings from settings file...
I:Loading settings from '/data/media/0/TWRP/.twrps'.
I:Backup folder set to '/data/media/0/TWRP/BACKUPS/015d2109a660180c'
E:Unable to open '/cache/recovery/.version'.
I:Unable to mount '/usb-otg'
I:Actual block device: '', current file system: 'vfat'
I:Switching packages (TWRP)
I:Set page: 'wipe'
I:Set page: 'action_page'
Formatting Cache using make_ext4fs function.
Creating filesystem with parameters:
Size: 464519168
Block size: 4096
Blocks per group: 32768
Inodes per group: 7088
Inode size: 256
Journal blocks: 1772
Label:
Blocks: 113408
Block groups: 4
Reserved block group size: 31
Created filesystem with 11/28352 inodes and 3654/113408 blocks
E:Unable to open '/cache/recovery/.version'.
Wiping data without wiping /data/media ...
I:Unable to unlink '/data/local/tmp/init.rc: Read-only file system'
I:Unable to unlink '/data/data/com.android.providers.applications/lib: Read-only
file system'
I:Unable to unlink '/data/app-asec/com.acrossair.tvguideuk-1.asec: Read-only fil
e system'
I:Unable to unlink '/data/app/org.mozilla.firefox_beta-1.apk: Read-only file sys
tem'
I:Unable to unlink '/data/property/persist.sys.NV_STEREOCTRL: Read-only file sys
tem'
I:Unable to unlink '/data/dalvik-cache/system@app@Books.apk@classes.dex: Read-on
ly file system'
I:Unable to unlink '/data/gps/glgpsctrl: Read-only file system'
I:Unable to unlink '/data/user/0: Read-only file system'
I:Unable to unlink '/data/system/entropy.dat: Read-only file system'
I:Unable to unlink '/data/backup/pending/journal-1737016036.tmp: Read-only file
system'
I:Unable to unlink '/data/sensors/KXTF9_Calibration.ini: Read-only file system'
I:Unable to unlink '/data/lightsensor/AL3010_Config.ini: Read-only file system'
I:Unable to unlink '/data/anr/traces.txt: Read-only file system'
I:Unable to unlink '/data/tombstones/tombstone_00: Read-only file system'
Done.
Updating partition details...
I:Data backup size is 1537MB, size: 6058MB, used: 4595MB, free: 1330MB, in data/
media: 3058MB.
I:Unable to mount '/usb-otg'
I:Actual block device: '', current file system: 'vfat'
I:Set page: 'action_complete'
I:Set page: 'clear_vars'
I:Set page: 'wipe'
I:Set page: 'action_page'
Formatting cache using make_ext4fs function.
Creating filesystem with parameters:
Size: 464519168
Block size: 4096
Blocks per group: 32768
Inodes per group: 7088
Inode size: 256
Journal blocks: 1772
Label:
Blocks: 113408
Block groups: 4
Reserved block group size: 31
Created filesystem with 11/28352 inodes and 3654/113408 blocks
E:Unable to open '/cache/recovery/.version'.
Wiping data without wiping /data/media ...
I:Unable to unlink '/data/local/tmp/init.rc: Read-only file system'
I:Unable to unlink '/data/data/com.android.providers.applications/lib: Read-only
file system'
I:Unable to unlink '/data/app-asec/com.acrossair.tvguideuk-1.asec: Read-only fil
e system'
I:Unable to unlink '/data/app/org.mozilla.firefox_beta-1.apk: Read-only file sys
tem'
I:Unable to unlink '/data/property/persist.sys.NV_STEREOCTRL: Read-only file sys
tem'
I:Unable to unlink '/data/dalvik-cache/system@app@Books.apk@classes.dex: Read-on
ly file system'
I:Unable to unlink '/data/gps/glgpsctrl: Read-only file system'
I:Unable to unlink '/data/user/0: Read-only file system'
I:Unable to unlink '/data/system/entropy.dat: Read-only file system'
I:Unable to unlink '/data/backup/pending/journal-1737016036.tmp: Read-only file
system'
I:Unable to unlink '/data/sensors/KXTF9_Calibration.ini: Read-only file system'
I:Unable to unlink '/data/lightsensor/AL3010_Config.ini: Read-only file system'
I:Unable to unlink '/data/anr/traces.txt: Read-only file system'
I:Unable to unlink '/data/tombstones/tombstone_00: Read-only file system'
Done.
Updating partition details...
I:Data backup size is 1537MB, size: 6058MB, used: 4595MB, free: 1330MB, in data/
media: 3058MB.
I:Unable to mount '/usb-otg'
I:Actual block device: '', current file system: 'vfat'
I:Set page: 'action_complete'
I:Set page: 'clear_vars'
I:Set page: 'wipe'
I:Set page: 'main'
I:Set page: 'clear_vars'
I:Set page: 'main2'
I:Set page: 'install'
I:Set page: 'flash_confirm'
I:Set page: 'flash_zip'
I:Set page: 'flash_zip'
Installing '/sdcard/pa_aosp_grouper.zip'...
Checking for MD5 file...
I:Cannot find file /sdcard/pa_aosp_grouper.zip.md5
Skipping MD5 check: no MD5 file found.
Verifying zip signature...
I:read key e=3
I:read key e=65537
I:comment is 1738 bytes; signature 1720 bytes from end
I:whole-file signature verified against key 0
I:Zip contains SELinux file_contexts file in its root. Extracting to /file_conte
xts
Creating filesystem with parameters:
Size: 681574400
Block size: 4096
Blocks per group: 32768
Inodes per group: 6944
Inode size: 256
Journal blocks: 2600
Label:
Blocks: 166400
Block groups: 6
Reserved block group size: 47
Created filesystem with 11/41664 inodes and 5415/166400 blocks
minzip: Extracted 2 file(s)
minzip: Error writing 32768 bytes from zip file from 0xbe95d794: Read-only file
system
minzip: Process function elected to fail (in inflate)
minzip: Can't extract entry to file.
minzip: Error extracting "/system/framework/framework-res.apk"
minzip: Extracted 418 file(s)
symlink: failed to remove /system/fonts/DroidSans-Bold.ttf: Read-only file syste
m
symlink: failed to symlink /system/fonts/DroidSans-Bold.ttf to Roboto-Bold.ttf:
File exists
script aborted: symlink: some symlinks failed
symlink: some symlinks failed
E:Error executing updater binary in zip '/sdcard/pa_aosp_grouper.zip'
Error flashing zip '/sdcard/pa_aosp_grouper.zip'
Updating partition details...
I:Data backup size is 1537MB, size: 6058MB, used: 4595MB, free: 1330MB, in data/
media: 3058MB.
I:Unable to mount '/usb-otg'
I:Actual block device: '', current file system: 'vfat'
I:Set page: 'flash_done'

Which says update fails because file system is read only.

I've tried Nexus Tookit and it says it was successful. Used the stock rom before the most recent one.

Flash Stock + Unroot...
------------------------------------------------------------------

erasing 'boot'...
OKAY [ 0.011s]
finished. total time: 0.011s
******** Did you mean to fastboot format this partition?
erasing 'cache'...
OKAY [ 0.022s]
finished. total time: 0.022s
erasing 'recovery'...
OKAY [ 0.022s]
finished. total time: 0.022s
******** Did you mean to fastboot format this partition?
erasing 'system'...
OKAY [ 0.032s]
finished. total time: 0.032s
******** Did you mean to fastboot format this partition?
erasing 'userdata'...
OKAY [ 0.028s]
finished. total time: 0.029s

sending 'bootloader' (2100 KB)...
OKAY [ 0.279s]
writing 'bootloader'...
OKAY [ 0.724s]
finished. total time: 1.004s
rebooting into bootloader...
OKAY [ 0.006s]
finished. total time: 0.007s

archive does not contain 'boot.sig'
archive does not contain 'recovery.sig'
archive does not contain 'system.sig'
--------------------------------------------
Bootloader Version...: 4.23
Baseband Version.....: N/A
Serial Number........: 015d2109a660180c
--------------------------------------------
checking product...
OKAY [ 0.040s]
checking version-bootloader...
OKAY [ 0.023s]
sending 'boot' (4896 KB)...
OKAY [ 0.644s]
writing 'boot'...
OKAY [ 0.018s]
sending 'recovery' (5432 KB)...
OKAY [ 0.720s]
writing 'recovery'...
OKAY [ 0.023s]
erasing 'system'...
OKAY [ 0.017s]
sending 'system' (529061 KB)...
OKAY [ 66.865s]
writing 'system'...
OKAY [ 8.887s]
erasing 'userdata'...
OKAY [ 0.026s]
formatting 'userdata' partition...
Creating filesystem with parameters:
Size: 6453985280
Block size: 4096
Blocks per group: 32768
Inodes per group: 8048
Inode size: 256
Journal blocks: 24620
Label:
Blocks: 1575680
Block groups: 49
Reserved block group size: 391
Created filesystem with 11/394352 inodes and 52512/1575680 blocks
sending 'userdata' (102525 KB)...
writing 'userdata'...
OKAY [ 51.792s]
erasing 'cache'...
OKAY [ 0.018s]
formatting 'cache' partition...
Creating filesystem with parameters:
Size: 464519168
Block size: 4096
Blocks per group: 32768
Inodes per group: 7088
Inode size: 256
Journal blocks: 1772
Label:
Blocks: 113408
Block groups: 4
Reserved block group size: 31
Created filesystem with 11/28352 inodes and 3654/113408 blocks
sending 'cache' (9052 KB)...
writing 'cache'...
OKAY [ 3.181s]
rebooting...

finished. total time: 132.412s

But It has no effect. It's still stuck in a boot loop and if I reboot into recovery it's still TWRP 2.6.0.0. I can browse data/data using ADB sh and all data still hasn't been deleted. When using ADB, I can push files to root but once I reboot the device they are gone. If I do ADB Shell mount after attemping to install someone via TWRP I get

rootfs on / type rootfs (rw)
tmpfs on /dev type tmpfs (rw,seclabel,nosuid,relatime,mode=755)
devpts on /dev/pts type devpts (rw,seclabel,relatime,mode=600)
proc on /proc type proc (rw,relatime)
sysfs on /sys type sysfs (rw,seclabel,relatime)
selinuxfs on /sys/fs/selinux type selinuxfs (rw,relatime)/dev/block/mmcblk0p9 on /data type ext4 (ro,seclabel,relatime,user_xattr,acl,barrier=1,data=ordered)
/dev/block/mmcblk0p9 on /sdcard type ext4 (ro,seclabel,relatime,user_xattr,acl,barrier=1,data=ordered)
/dev/block/platform/sdhci-tegra.3/by-name/APP on /system type ext4 (ro,seclabel,nodev,noatime,nodiratime,user_xattr,acl,barrier=1,data=ordered)
/dev/block/mmcblk0p4 on /cache type ext4 (ro,seclabel,relatime,user_xattr,acl,barrier=1,data=ordered)

If I then go into the mount menu and remove ticks in boxes and put them back I get

rootfs on / type rootfs (rw)
tmpfs on /dev type tmpfs (rw,seclabel,nosuid,relatime,mode=755)
devpts on /dev/pts type devpts (rw,seclabel,relatime,mode=600)
proc on /proc type proc (rw,relatime)
sysfs on /sys type sysfs (rw,seclabel,relatime)
selinuxfs on /sys/fs/selinux type selinuxfs (rw,relatime)
/dev/block/mmcblk0p9 on /data type ext4 (rw,seclabel,relatime,user_xattr,acl,barrier=1,data=ordered)
/dev/block/mmcblk0p9 on /sdcard type ext4 (rw,seclabel,relatime,user_xattr,acl,barrier=1,data=ordered)
/dev/block/mmcblk0p4 on /cache type ext4 (rw,seclabel,relatime,user_xattr,acl,barrier=1,data=ordered)
/dev/block/mmcblk0p3 on /system type ext4 (rw,seclabel,relatime,user_xattr,acl,barrier=1,data=ordered)

but if I try writing to cache, system, sdcard, data, it instantly switches back to ro and faiils. ADB push says it succeeds and file appears on device when it is mounted as RW, but is gone on reboot.

If I boot into recovery TWRP 2.6.0.0 and type adb devices, I get

List of devices attached
0123456789ABCDEF recovery

Which obviously I know is iffy.

If I do fastboot boot <TWRP 2.6.3.0>

and do adb devices, I get

List of devices attached
015d2109a660180c recovery

If it means anything, previously i've taken screenshots on the device and deleted others. Then connected to a PC in normal mode and what I see in the screenshot directory was from before those changes.

If it also has a bearing, when I connect the Nexus to the PC it tells me it can perform faster when connected to a USB2.0 port which it is. It Also has the power recharge problem, to get it to recharge I have to plug the usb cable in, remove usb cable and reinsert within 10 seconds, turn the screen off and leave it alone. As solution posted on Google Forums, but it used to charge normally.