[Galaxy S 4 Active Q&A, Help & Troubleshooting] Devo7v:
It sounds like you have quite a bit more reading to do so that you can understand exactly what you are trying to do. That said I'll try to answer your questions.

Is TitaniumBackup the only root app you've used, have you frozen anything, installed any mods, or messed with any of the apps in your system/app folder? This will become important later.

It sounds like you need to uninstall BusyBox. Normally SuperSU will uninstall this but it sounds like you tried a different method of unrooting that may have left bits in your system and since you weren't technically rooted anymore SuperSU didn't know what it needed to do.

It sounds like you have the AT&T i537. This phone has a locked bootloader as you know. AT&T has required Samsung to lock down the i537 and will not allow them to release any firmware on Kies, this is why the software says your phone is incompatible. Basically AT&T is screwing us hard.

The website you linked to is giving you bad information. The MI2 file is not technically "Official Firmware". This is a pre-release version of the firmware that DesignGears was able to get for the community. This will become important below.

As you've stated, this MI2 zip file that you've downloaded has a single exe file in it. This exe file should be run from a computer and it will allow you to flash new firmware to your phone. BUT, as I mentioned above this is pre-release firmware. What that means is you will forever be stuck on this firmware, you will not be able to take official updates from AT&T or Samsung. If you're ok with that, then go ahead and flash your phone with the pre-release of 4.3. If you want the official 4.3 update you have a little work to do. Above I asked you if you messed with any of the files in system/app, this is because the official update file can be downloaded and can even be flashed but it checks nearly every file in the system/app folder to make sure that it is the original file. If you've modified anything in there, the update is going to fail.

I'm going to post a few links of stuff you should read, but there is definitely a lot more that you should be reading.

How to flash stock MF3 - this is most likely the firmware you are on, but this thread will tell you how to get it back to stock, the way it was when you took it out of the box. This should allow you to take the official 4.3 update if other methods don't work.

MF1 Pre-release (4.2.2) - this is a pre-release of 4.2.2, you should read this.

MI2 Pre-release (4.3) - this is a pre-release of 4.3, read this thread to understand the benefits and drawbacks of flashing this pre-release firmware.

Official 4.3 Update Thread - this tell you what you need to do to try to update your phone to the official version of 4.3. Currently there is to way to root the official 4.3.

SafeStrap Thread - this will allow you to flash TouchWiz 4.2.2 based ROMs on your phone. Again, you need to read before you do anything. There's actually a lot we can do even though our bootloader is locked.

I can't stress enough how important it is to read. Once you've read everything and you think you understand what you're doing, READ MORE. There's always somebody who's done what you're trying to do and someone has more than likely given the answers you're looking for. Read as much as you can and you can avoid bricking your phone and ending up with a paperweight.

Good luck and us know if you have any questions, everybody is here to help.