Disabled apps wouldn't cause a problem. You do realize that you have to unroot first, and you won't be able to regain it, right? The update locks the bootloader and there are not currently any exploits to get around it. Curiously, there is a workaround for the updated S4 Active though. I guess it's just a matter of time for the S4.
To answer your question about how to tell whether you deleted system apps, you'd have to look at the manifest file and compare it to what you have in your system folder. There might be an easier way, but I don't know it.