Revert to El Capitan

Question

I'm having major 'disagreements' with Sierra, compatibility issues with software etc, & have decided to revert to El Capitan.

I have done this many times in the past, tested an OS then gone back to the earlier version. I make a clone of the old drive, then update; clone back after a few days & all is well. Most I lose is a few non-essential emails which doesn't bother me.
This time, I've left it too long to do that. My clone is 2 weeks old, my POP email will only sync back one day. I have no real trace of what else may have changed in that period, but let's say with the best of intentions I'll miss something that I later discover I should have made a safety of.

I have Time Machine, up to date, but of course it's now syncing Sierra.
I also have Backblaze.
So ultimately I should have the resources to go back & find anything I may have missed.

My worry is if I use a clean install & migrate from Time Machine, some old authorisations on the drive will be lost. Some cannot be retrieved if they break because the servers that authorised them no longer exist. [Old pro audio plugins etc, still working but no longer supported.] These survive a clone, but I don't know if they'd survive a migrate. [I didn't migrate from my old 3,1 to this 5,1, I just moved the boot drive from the old to the new machine.]

I have all old installers in my Purchase History, so obtaining El Capitan is not an issue.

I'm on a Mac Pro 5,1 so dropping in a spare drive is no problem, if that would help.
I've never tested whether this machine will boot from USB, my older 3,1 never would - I shall test that & update the question.
Edit I've tested, it will successfully boot from an El Capitan installer USB. I've also made a clone of the boot drive as it is right now, belt & braces.

I see my options as...
1. Restore from the clone & try to find anything I missed.
2. Nuke & pave, then migrate Time Machine

Is there a 3rd option?

Some method to restore to my current backup, but sitting on El Capitan rather than Sierra?

Late Edit
Well, option 2 just went away. The installer simply refuses to migrate from a newer OS to an older one, whether from a mounted or remote drive, or Time Machine.

Restore Mavericks from Time Machine may help future Googlers too.

Answer 1

Next time I'll remember to set my POP3 server to keep mails for a month before I ever upgrade again :/

Simplest solution seems to have been to re-clone back from my two-week-old El Capitan clone - the one I made right before the upgrade.
That successfully took me back to El Capitan - but from 2 weeks ago.

That left me with having to remember/pick through what had been changed in the past two weeks.

Carbon Copy Cloner makes a Safety Net folder containing older versions - though in this case it was more useful for finding newer versions of apps I'd updated in the meantime.
Mainly what it had dumped in there was "Sierra".

My most important stuff was my photography folder, so I simply copied that in its entirety from a safety copy [yesterday's Sierra clone].

A Parallels VM I knew I had been working on I did the same.

Because Mail had changed its library structure I lost two weeks of relatively unimportant emails - I can live with that. If I remember anything hugely important I can boot to my Sierra clone & forward it to myself.
Time Machine proved to be completely useless in that respect. It claimed to be able to restore missing emails, but as everything in the past two weeks was in a newer format, it couldn't actually find anything.

So, job done. It actually took about 45 mins in all; once I'd figured out the structure & the potential sacrifice.

The moral of the story... sometimes two clones & two complete backups still isn't enough to get back all data.

I'm still open to alternative suggestions.
I'm in a position to simply repeat the process, as I still have copies of all the 'originals'.

Answer 2

You could look into using an installation of El Captain on a separate partition, which should give you access to your files and enable you to test what you can successfully migrate to that OS if you need to, if not (and providing your partition is large enough) you could likely just boot to (and use) El Captain from there. I encourage you to do some additional reading before you jump in.

...be sure to back your data up first, I believe this would be essentially a non-destructive effort.