I am currently on MJA software, MJA baseband, ktoonsez kernel, MJA build #, but have the MF9 bootloader yet. Can I simply update the ROM and nothing else, maintaining root and all my current settings?
I don't know - I didn't chance it. I did a nandroid backup, backed up my Nova settings, backed up my SMS messages...basically backed up all the configs I could to my SD card.
Then I used Philz recovery - did a "wipe to install a new ROM", wiped Dalvik cache, wiped everything else again just for good measure.
Then I installed the software update via Philz, and rebooted into download/flash mode (there's an option in Philz to do that).
Then flash the MK2 modem using Odin - uncheck reset clock and auto reboot. When I got the "PASS" I did a battery pull and booted the phone.
When the phone came back up, did the initial setup (skip setting up gmail and other accounts until after you've disabled auto update and auto download apps in Play Store), and shut down. Flashed SuperSU 1.86 and booted again. Installed Root Explorer and deleted all the Knox crap (instructions in first post).
Installed TiBu. Disabled/Froze bloat through system or TiBu. Reinstalled all my apps from the appstore and restored settings and SMS from the saves on my SD card.
This update has the stock kernel, but it works and there are no WiFi issues. I was using the KT kernel on MJA, but only because there were WiFi issues - every time I tried to tweak something my phone would go all unstable and wonky so I just left all the tweaker settings alone. This update is already rooted as well, but you will need to re-flash the newest version of SuperSU before it will work (instructions in the link to SuperSU in the first post). As long as you still have custom recovery and MF9 bootloader you won't lose root and if you do, you can regain it pretty easily.
Make sure the modem update takes - I actually ended up doing it twice (first time with autoreboot and reset clock enabled didn't take). If the modem update doesn't work you WILL have WiFi issues until it updates successfully.
MK2 is running MUCH better than MJA. I had all kinds of problems on MJA with iffy performance, sudden crazy battery drain, and hard crashes when getting phone calls. None of that now and everything is running much smoother.
