Appreciate the detailed, and informative, update. As I have stated numerous times before, I use SuperDuper! for my backups. When I recently obtained my new Samsung 860 EVO 500 gig SSD and installed it inside an external case, I connected it to my Mac Mini (via USB 3.0), and used Disk Utility to Erase and Format it. The Format is APS, and the Scheme is GUID Partition Map. I then downloaded and installed OS 10.14 (clean, fresh, "virgin" installation) onto that SSD. Finally, I "migrated"/copied needed "things" (that was offered as part of the Mojave installation (same as always)) from my latest SuperDuper! backup (done about 3 days prior). I then restarted my Mac Mini from that external SSD, and everything was fine. All my Thunderbird EMails "came over", as did all of my 1Password V7.2.1 data, and all my other files/folders, etc. (Except for Tech Tool Pro and the High Sierra version of Onyx, all my other applications are compatible with Mojave. Removed Tech Tool Pro after that installation, and obtained the Mojave version of Onyx).
When I upgraded to OS 10.14.1 "in place", everything remained the same. And earlier today, while in that Mojave "environment", I downloaded, installed, and ran the new Mojave version of Onyx. As expected, worked like a charm.
My backup "needs" are rather simple, as I just backup once a week. I don't keep any prior versions of my backups, and do not do any "in between" backups. For example, when I do my backups tomorrow, SuperDuper! will delete the prior one, and "replace" it with the new one. I of course have no experience with Time Machine backups, so really cannot help you with that "issue" (if there are issues).
Not sure if you saw the thread I recently posted about OS 10.14.2 being in beta testing, and maybe someone else can help you with Time Machine backups (especially if you are doing any "in between/update" "backups"). There are some folks on here who use both Time Machine, and either SuperDuper! or Carbon Copy Cloner. One thing you might try is the following:
1. Download the full OS 10.14.2 installer file from the App Store when it becomes available.
2. Download SuperDuper! from here:
https://shirt-pocket.com/SuperDuper/SuperDuperDescription.html
You can use it in demo mode, and it has full functionality.
3. Do "final" disk cleanup/maintenance/repair tasks.
4. Do a SuperDuper! backup to an external device. That will include the "install macOS Mojave" file from step 1, along with all your files. folders, settings, etc. from your Mojave OS 10.14.1 setup.
5. Restart your Mac from that SuperDuper! backup.
6. Use Disk Utility there to Erase and Format your internal drive.
7. Navigate to that (new, ie, V10.14.2) "install macOS Mojave" file, and do a clean, fresh installation of OS 10.14.2 onto your internal drive.
8. Finally, "migrate"/copy needed "things" from that SuperDuper! backup.
9. Restart your Mac.
All of that is just a suggestion, but it is based on my experience with my "flat", once a week SuperDuper! backups. And given that we both use Thunderbird and 1Password, my experiences could be helpful.
As far as your "keychain" issues with 1Password, I hope I am not having such issues. I think what I might try before I finally update to Mojave, V 10.14.2 (via a clean, fresh installation), is to do step 1, and steps 3 through 9 above, for my "test" external SSD. In fact, I just might do that even if the Mojave-compatible version of Tech Tool Pro is released then also. I just want to insure I do not have the 1Password issues you encountered.
I guess there is one other "caveat" to possibility consider. Given how much work you needed to do to finally get things working as you expect (yes, I realize you have some more to do, but hopefully that will be over soon), just hope your "final" OS 10.14.1 environment is "clean" enough, as that is what you will be copying/cloning with SuperDuper! in step 4 above.