Can I update the OS manually? Will I need to restore to stock to update to the latest OS every time?
So i'll clarify a little bit now that I'm at a computer and typing is faster.
OTA's are typically what are called Differential updates. What that means is that they aren't an complete re-install, they contain only what has changed since the last update. Normally that's fine because you don't want to re-download and re-install a whole OS when all that's changed is a fraction of it. But when you are hacking up your phone you can run into problems because doing a differential update on an OS the isn't the one you are expecting leaves you ripe for problems. To prevent that Google looks at the "state" of your system and if it passes checks, the OTA is allowed to install.
When you have a custom recovery one of those checks fails but even simply installing root apps that might change how the system behaves or functions could trip another check and prevent the OTA from installing. All of that is simply to say that going back to the old recovery might not be enough to allow the OTA to install and even if it is...you'll still have to re-root.
So back to your latest question. Is there a way to "manually" install the OS, yes there is. It's called a system img and they are posted by Google usually days to weeks after the latest version is released. These images are our safety net, they are what allow us to completely return to stock when, not if, we completely screw something up.
These images are what the toolkits use to "restore" your phone. In fact all any toolkit is, is a user interface on top of all of these commands the phone already has. it just makes using them a little easier because they are button clicks instead of command line.
Now back to your immediate situation, you want to take an OTA update...Well right now there isn't an OTA so you don't have to worry about it yet and have some time to plan.
This is what I would do in your situation.
1) Install Tibu and back up all my apps, offload them to a PC or to DropBox so I have them. Just keeping them on the sdcard won't work because that'll get wiped if you restore the phone.
2) Wait for the OTA and try to install it. Best case, it installs, you re-root and you are done. Worst case it jacks your phone and you have to restore it. What is most likely though is that it won't install.
3) if it doesn't install or it wipes your phone you have a few options. I would probably completely return to stock 4.2.2 and then wait for the OTA (or is someone has the OTA zip you can install it manually with the stock recovery, theyll post it hrs after the OTA hits and it'll have instructions. You'll need to be stock to install it for all the reasons i said before. It's still the OTA its just the manual install)
4) Once it's installed I would re-root....move the TiBu backup over to the phone and restore the apps i don't want to reconfigure again.
You could also just try to install the OTA...if it fails...wait for the images to hit and then do a full restore up to the new version but that would require patience and I do not have that

It also takes a while for the toolkits to update with the newest images.
That's my two cents man. Bottom line is that these phones are pretty damn forgiving so no matter how you proceed or what you screw up, as long as you have a good TiBu backup the most you lose is your time and maybe some hair
Don't hold your breath for an OTA either. They take longer than everyone wants every time. I'm sure it's coming but its not uncommon to hear "OTA today!" 3-5 times before it actually hits and then it's a staged rollout so you may not see it right away anyway. And right now we barely know anything about the next version so no one really knows what they are excited about, other than rumors.
Hope that helps!
