The option you see I think would be the best solution.
Let's first try something
Reset SMC https://support.apple.com/en-us/HT204063
Reset NVRAM https://support.apple.com/en-us/HT201295
Turn on your Mac and immediately hold Shift so it boots in Safe Mode. It's a bit longer boot because macOS will do some maintenance under the hood and can fix some problems just like the one you have.
Once up, restart normally and see if macOS got back in track.
If it doesn't work, then yes, try a clean install. By clean install I mean wipe the entire disk and install it from zero.
As you have and external clone drive, you don't need a bootable USB installer. Boot from your clone, copy your personal that from the Mac drive, download the macOS installer, run it and choose to install on the internal drive.
Erase the Mac disk https://support.apple.com/en-us/HT208496 (make sure to select the correct drive to wipe, I know it's kinda obvious, but I saw people make some mistakes in time, so just be sure, OK)
About TM, I'd say for you not to recover from it
Make the clean install of macOS, let it update everything it asks for, install your favorite apps... and then activate the TM
But here some very important steps
Turn off automatic backup just for now
Set your old TM drive as your TM again
Note that the backup file on the TM disk has a name, for exemple, "pastor s.backupbundle"
Go to System Prefs > Sharing and name your Mac as pastor s (that was the name of your Mac when you created the TM you have).
Now back to the TM, if you open it, you'll see your Mac recognizes it as if it was your current TM, so you can open it with that particular TM interface, with a timeline on the right.
Now copy back your personal data from there.
Once it's done, you can redo your TM, start a new TM backup bundle file and also your clone drive, so they all will be in line with your new installation.
Yes, bit of a hard work, but this will allow you to have a clean install, free from old debris and maybe corrupted files and configs from previous system and updates that could affect the perfomance of your Mac.