[Verizon LG G3] ohlin5:
I can't speak to the IMEI clearing as being a "common" issue....I've restored at least 5 different phones using the tot method, several multiple times and never once had an issue. I do, however, maintain a backup in the cloud of the EFS partition (same basic thing I think? I just know it's an important partition lol) for every phone I oversee and have messed with.

As for your question about stump/bump/etc., there are several different root methods out now...."Stump root" was just the name of the first - and so it's what I've always stuck with. "Bump", on the other hand, is the method for "unlocking" the bootloader and flashing TWRP.

As for the play store 'auto' app, I hadn't even heard of it until you said something and I searched. I'm assuming you're talking about this. All I can say is that I've never used it so I have no idea. Below I've laid out the steps that I, personally, follow each and every time I've gotten a new device or restored one. I realize there may be simpler ways out there now, but I've been in this specific community since the very beginning, and so I've just stuck with the "tried and true" stuff that came out first.

As for the one click TWRP installer on the play store, again I don't know. However, flashing the "bumped" TWRP via flashify is probably the easiest way to do it (it is not officially stated by the devs to work, but countless people including myself numerous times have confirmed it does).

So, TLDR:

If I were to get a brand new, VS985 today, here is the exact set of steps I would follow (I just got another one 2 weeks ago and these are what I did, and have always done):

1). Use the tot method, found here to restore (downgrade) back to the initial stock release software (version 10B_03). Alternatively, you can use the "kdz" method found here, but on my Windows 7 PC the tot method has always worked like a charm and the one time I used the kdz method it seemed a bit sketchier, but to each their own. I think the main "push" for the kdz method was that some people were having trouble getting the tot method to work on computers w/ Windows 8/8.1.

2). Once that's done, reboot and do minimal setup, then use stump root (found here) to root. Follow the directions exactly, and as long as you're on 10B it will still work - it's just been patched in newer software versions. After rooting and rebooting, then install superSU from the play store, open that, update the binary via "normal" method and then reboot once more. After that reboot, uninstall the stump app, you don't need it anymore.

3). Then, install Flashify from the play store. To be safe, I usually open it and make sure I've granted root, then close it and open superSU and make sure it's got the green mark next to it signifying it has full root access (again, just to be sure). Then, download the "bumped" TWRP image from here, and put it somewhere you can find it on your INTERNAL storage (not sure if this is vital, but again, just being safe). Also, for later, download the zip of TWRP 2.8.6.1 from here

4). Use the Flashify file browser to flash that recovery image you just downloaded to the your internal storage. Let it do it's thing, then reboot when it prompts you.

5). You should now boot up into TWRP. Use the install function to update from the TWRP you just flashed (2.8.0.0) to the 2.8.6.1 zip you just downloaded. Then use reboot>recovery to confirm it took.

6). That's pretty much it. With that you're fully rooted + unlocked. Only other thing I would highly recommend at this point is following the guide here to back up your EFS partition, and then store it to your Google drive or dropbox or other cloud storage or somewhere safe lol. If you're gonna stay stock I'd freeze the system update apps, or better use just flash skydragon or jasmine roms as they're great stock-based roms.

Any other questions just let me know.