Since I did not backup the application I had no way to use the OTA, however after a few hours research I found out a method to completely restore the system to stock.
Part 1: Restoring Tablet to Stock
1. Download the system dump that matches your current software:
WW - http://dlcdnet.asus.com/pub/ASUS/Eee...teLauncher.zip - MD5 - 68D41197B399967B7F6789E47683A0D7
US - http://dlcdnet.asus.com/pub/ASUS/Eee...teLauncher.zip - MD5 - DF17D3129378E9A7F81C58AF7BF5396B
TW - http://dlcdnet.asus.com/pub/ASUS/Eee...eLauncher.zip- MD5 - 3999B0E052211AA53ED1DB5D06A02AD3
2. Unzip the compressed firmware file to the root directory of a MicroSD card (external). Only extract this once so your sdcard should look something like this:
3.With your Transformer turned on, insert the MicroSD into the MicroSD card slot.
4. An exclamation mark should appear in the notification area.
5. Tap the mark and proceed with the update.
6. Your tablet should now reboot and proceed to update the tablet, if you get an error try redownloading the update and trying again.
Part 2: Rooting your Tablet
Voodoo root keeper didn't save my root after part 1, so to root it I used Debugfs automated root:
After your tablet is rooted you should use OTA root keeper to backup your root.
Part 3: Manual Update to Jellybean
1.Download the dlpkgfile for your system, I uploaded the US file: <--------------- US ONLY don't try if your tablet is not on US firmware, it might brick
WW version dlpkgfile <--------------- WW ONLY don't try if your tablet is not on WW firmware, it might brick
The WW update file (thanks for kikistans for uploading):
2. Place the dlpkgfile on your tablet's storage, MAKE SURE THE dlpkgfile does not have a .zip extension, the file has no extension!
3. Download ES File manager and go to settings>root settings and tick all the boxes.
4. Copy dlpkgfile to /cache
5. Go to /cache/recovery and create a new file named command
6. Open the file as a text and place the following code in it and save:
7. Turn off the tablet
8. Press and hold volume down+power until the tablet vibrates then release power and keep holding volume down
9 When a text shows on the boot logo screen release volume down and click volume up
10. The tablet should now start updating, it'll take about 30 minutes and once the tablet boots you'll have jellybean
11. Restore root with root keeper
This method should work for everyone with a locked bootloader
Sorry I've been busy, it seems like some people are missing 3 files, follow this thread if you're missing those files:
Also some people are reporting that their tablet is get bricked, MAKE SURE THAT YOU'RE USING THE RIGHT FIRMWARE UPGRADE
new-tilus has reported that this method worked for his stock unlocked tablet.