Preparation:
1. Create a working folder, for example pre-rooted, download and extract
THIS (64 Bit) file and copy/paste (simg2img & ext2simg) into working folder.
2. Download SuperSu.zip from Chainfire's thread and extract all files to new folder, for example "root files". Copy/paste this folder into working folder.
3. Download any Samsung FW and extract it. You'll have a single file xxxxxxxxx.tar.md5, extract it again to new folder (keep name of the folder same as name of your FW, xxxxxxxx , it makes things easier to work with).
4. Go to the new folder and check if all files are there (5-10 files), look for system.img.ext4. If everything is there, copy/paste whole folder xxxxxxxx to your working folder /pre-rooted
5. Move system.img.ext4 directly to the working folder: /pre-rooted/system.img.ext4.
At this point, you should have following files/folders in working folder:
/pre-rooted/system.img.ext4
/pre-rooted/ext2simg
/pre-rooted/simg2img
/pre-rooted/xxxxxxx (folder with your FW)
/pre-rooted/root files (folder with extracted files from SuperSU.zip)
Pre-Rooting process:
Open Terminal and navigate to the pre-rooted folder, for example: cd /home/*username*/pre-rooted.
Step 1:
Convert system.img.ext4 into a raw system partition that can be mounted under Linux as r/w partition - system.img.raw
Type in Terminal and press Enter:
Code:
./simg2img system.img.ext4 system.img.raw
and wait until the process is finished, it takes few minutes....
Step 2:
Mount converted partition under Linux:
Type in Terminal and press Enter:
Code:
mount -t ext4 -o loop system.img.raw /mnt
Use any File Manager or just navigate to /mnt/.... and there you have full access to the system files.
Step 3:
Copy/paste or delete any files you want from/to system, for example root files:
Superuser.apk -> /mnt/app/Superuser.apk
su (binary) -> /mnt/xbin/su
daemonsu (binary) -> /mnt/xbin/daemonsu
.su (binary) -> /mnt/bin/.ext/.su
recovery.sh -> /mnt/etc/install-recovery.sh
libdummy.so -> /mnt/lib/libdummy.so (extra file, can work without it)
Step 4:
Setting up permissions. Use Terminal, type and press Enter after each line:
Code:
chmod 06755 /mnt/xbin/su
chmod 06755 /mnt/bin/.ext/.su
chmod 0755 /mnt/xbin/daemonsu
chmod 0755 /mnt/etc/install-recovery.sh
chmod 0644 /mnt/app/Superuser.apk
chmod 0644 /mnt/lib/libdummy.so
Step 5:
Setting up SELinux markers (for JB 4.3 onwards). Use Terminal, type and press Enter after each line:
Code:
chown root.root /mnt/app/*
chcon u:object_r:system_file:s0 /mnt/app/*
Step 6:
Rebuilding system partition back into system_new.img.ext4. Use Terminal, type and press Enter
Code:
./ext2simg -v ./system.img.raw ./system_new.img.ext4
Partition size will be automatically adjusted, according to the size of system.img.raw (it takes few minutes to finish)
Now, just copy/paste system_new.img.ext4 to your FW folder - xxxxxxx - and rename it back to system.img.ext4.
Repacking all files back to new_xxxxxxx.tar.md5:
1. Use Terminal and navigate to your FW folder: /pre-rooted/xxxxxxx
2. Packing it all up:
Use Terminal, type and press Enter:
Code:
tar -H ustar -c aboot.mbn boot.img cache.img.ext4 hidden.img.ext4 modem.bin NON-HLOS.bin recovery.img rpm.mbn sbl1.mbn sbl2.mbn sbl3.mbn system.img.ext4 tz.mbn > I9505XXXXXXXX-PRE-ROOTED.tar
this is example of complete FW for GT-I9505, all files (bootloaders, modems, etc..) are listed and included. Check your FW folder for correct list of files from your FW.
3. Generating and adding .md5 checksum:
Use Terminal, type and press Enter after each line:
Code:
md5sum -t I9505XXXXXX-PRE-ROOTED.tar >> I9505XXXXXXX-PRE-ROOTED.tar
mv I9505XXXXXXX-PRE-ROOTED.tar I9505XXXXXXX-PRE-ROOTED.tar.md5
That's it!! All done, you can now use Odin and flash your new, pre-rooted FW.
NOTE: Make sure that you have Original FW on your HDD, just in case if your new FW won't boot up! 
Also can you also deodexed and prerooted the MK2 version? thank you sir.
