You learn something every day!!
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Now I presume that would be Mojave, for instance, asking me *if* I want to migrate files, and then apparently it is smart enough to go out to my previous CCC clone of Sierra and migrate over applications, app settings, preferences, email, bookmarks, and all of my data, huh?
That is really hard to believe that it can do that, and that it actually works, but since you say you have done it before, that is good to know!
Yes, and that is true for ANY version of the Mac OS that 1) you install, and 2) want to migrate from (via the bootable backup/clone created with SD or CCC). I did exactly that with at least the last 6 versions of the Mac OS. Last year I went from High Sierra to Mojave, and then more recently from Mojave to Catalina.
But again, it is best if you do the following tasks first:
1. Insure all your third party applications are compatible with the OS you are moving to (in your case, that would be Mojave). That might mean you'll need to either download (and can possibly apply) updates for such programs, or in the case of Onyx (there are probably some others), download the version specific to the OS you are moving to.
2. Before you do the SD or CCC backup, do as much disk cleanup/maintenance/repairs as you can. Myself, when I embark on such a project, I first run Onyx and Tech Tool Pro on that last (and soon to be backed up) system I have. I then do my SD backup/clone to a partition on an external SSD.
Now, as I mentioned, the one possible "unknown" is if some (or all) of your issues are caused by a "bad" application (or applications). That is a more difficult problem. If you have been diligently upgrading such applications, that issue should be minimized. And hopefully it is not due to any bad Apple apps. That would be a real bummer!
I will mention one other thing. I have always done such a migration for the just prior version of the Mac OS to the new one. Thus, I did it from High Sierra to Mojave, and then later on, from Mojave to Catalina. I see you will want to do it from Sierra to Mojave. Hopefully, that will be OK, and work fine. One thing to be aware of is that the APFS File System was introduced in High Sierra, then further "refined" in Mojave and Catalina. You should be OK.
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To try and tackle my audio issues, I'm just going to install a recent clone of Sierra on my other Retina, and see how things go from there.
Personally, I am old school when I build a machine and I do everything from scratch, and manually.
Most people rebuild their computer because they start having issues, so why copy over crap to a virgin machine. (I know you Mac types will say, becuse "it just works", but I am skeptical.)
This is another reason I am very slow to upgrade - because it turns out taking days to do.
Fortunately with macs, they just go one and on, so it's a rare occurence.
For the reasons you state, that is why I make a concerted effort to keep my machines "lean, mean, and clean". That involves daily cleanup, and most of it comprises the permanent removal of deleted EMails. I use Thunderbird for my EMail client, and it is easy to do that task. Also, if I download a newer version of a program, I save it to a folder I have called "Useful Software" (it contains folders for each program I use, along with just programs themselves). In most cases, each such program folder contains at least the current version of the program, so after placing the new version there, I get rid of the prior version (some programs I keep both the current and prior versions). I also have another folder called "Upgrades", and there I have folders for the current Mac OS, and the prior one, and for Tech Tool Pro. Again, that is where I keep both original installer files, and updates. And again I don't keep too many prior updates.
Finally, of course, as I already mentioned above, every Saturday I run Onyx and Tech Tool Pro for more disk cleanup, maintenance, and repairs, and then make 2 backups/clones via SuperDuper! to 2 separate, external SSDs.
All of that is second nature to me, and it has consistently resulted in me having no issues with my systems. But if I did not do a lot of that, then like you, if I were to do a clean installation, I would need to do a one by one installation of all my software. Then of course there are all the settings, passwords, etc. Definitely a chore, just like you are indicating. Hence, that is why I will continue to be diligent.