[Galaxy S 4 Mini Q&A, Help & Troubleshooting] fire3element:
Well no one was able to answer my question, so I had to figure it out on my own. Hopefully the following information will be of help to someone else without spending 36+ hours digging through the internet for answers.

You CAN fix your phone it you are on the NJ1 kernel. This is NOT a guide to fixing a bricked phone, although it may fix that too.

If you are on the NJ1 kernel, there are no root methods currently available. You MUST be on NE3 or lower. I also attempted to flash the custom recovery through Odin, but after a reboot it was as if I did nothing. No Knox flag, no warranty trip, no custom recovery.

Here is what I did to get custom recovery and root:

READ THIS BEFORE ATTEMPTING STEP 1.

This is only for the Sprint variant of the S4 Mini. Model number SPH-L520

Your Warranty could be voided. Proceed if you like. (More info on steps 5 and 6)

I had a horrible time getting the downloads from Sammobile. You WILL have to create an account and login to download files. I could not find any working links for the firmware below except for this site. Register a user name and password, DO NOT UNCHECK THE BOX that says receive emails from Sammobile OR YOU WILL NOT GET YOUR REGISTRATION EMAIL. On the Register page it is at the bottom. After you register, check your email and click on the link to complete the registration.

Close all your windows that are open to sammobile.

You are going to want to download Internet Download Manager in order to download files from Sammobile. After many many attempts to download the firmware from Sammobile, all tries failed. YOU ARE GOING TO NEED IDM to get a reliable download.

Download IDM ---> https://www.internetdownloadmanager.com/download.html

Install it and follow these directions to enable resume downloads in IDM ---> http://xdaforums.com/showthread.php?t=2765456

If you do not do the steps above, you most likely will have failed download after failed download.

Even after setting this up, the firmware download failed on me twice. I deleted it from the download list in IDM and started it again.

IDM integrates well with Internet Explorer. Kinda buggy with Chrome. I would suggest using IE for the rest of this Tutorial.

Ok, now that you have that squared away, move on to step 1

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1) Flash your phone back to NE3. You can get that here ---> http://www.sammobile.com/firmwares/download/31482/L520VPUBNE3_L520SPTBNE3_SPR/ (click Regular Download, then on new page right-click Confirm Download and click SAVE AS. After that the IDM window should pop up. Just Start Download)

Also go ahead and download download the NJ1 in case things get rough. List of all firmwares here ---> http://www.sammobile.com/firmwares/database/SPH-L520/

2) Download and install the Samsung drivers ---> http://www.mediafire.com/download/a4hd8y0c1iakysk/Samsung-Usb-Driver-v1.5.49.0.exe

Download Odin 3.09 ---> http://androidhost.org/PVAIv

Unzip Odin to a folder or desktop. Do not run it from in the zip folder.

3) Run Odin 3.09.

Reboot your S4 Mini SPH-L520 into download mode. Turn phone off > Hold Volume Down, Home Button, and Power Button all at the same time. Wait for the phone to buzz and the pop up on the screen. Release the buttons and press Volume Up to confirm.

Now plug in your phone to your computer. It might take a few seconds for the drivers to install. Wait until Odin shows blue color in the first bar on the left side. Should say 0:[COM3] (the COM number will be different depending on your computer and the USB port you plugged it into)

VERY VERY IMPORTANT! Make sure that the AUTO-REBOOT and F. RESET TIME boxes ARE checked. Make sure that the RE-PARTITION box is NOT checked.

4) Unzip the NE3 download from earlier. Click on the AP button in Odin and navigate to where you unzipped NE3. It should be a .MD5 type of file

Give Odin a few mins to check the file. It may appear that Odin has hung up, just be patient.

After Odin has run the check, it should say ok in the little window on the bottom left. Now click START and wait.

DO NOT bump the phone, the laptop, the usb cord, and MAKE SURE THE BATTERY DOES NOT FALL OUT!!!

After Odin is done flashing, it will reboot the phone. After the initial reboot, the phone will reboot itself once more. Be patient

Now wait for the phone to completely boot up.

5) After you have got back to ME3, you can follow this guide to root it ---> http://androidxda.com/root-samsung-galaxy-s4-mini-sprint-sph-l520

You already have most of the files you need. Just follow the instructions and download what you do not have already.

By the way, in Odin the AP button and the PDA button are the same

(This method should not trip the Knox counter, but I am unsure. Mine was already tripped before all of this)

OPTIONAL (this will trip the Knox counter and lose warranty status)

6) Now you can use this guide to install the custom recovery ---> http://techbeasts.com/2014/05/04/in...-root-sprint-samsung-galaxy-s4-mini-sph-l520/

Again, you already have most of the files you need. DL what you don't have.

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I am planning on instaling CM11 ---> http://xdaforums.com/showthread.php?t=2669991

This ROM apparently needs a specific recovery in order to work properly. I installed that one instead.

MAKE A BACKUP IN THE RECOVERY OF THE STOCK ROM BEFORE FLASHING ANY CUSTOM ROMS, or else be sorry later.

This is about as simplified as I could get it. Hope this helps out those of you that were as confused as I was.

I will not be providing support. Simply do not have the time. There is more than enough info here to help you figure out what to do.