I understand about updating your recent responses, but what I was referring to is which 3rd party utilities did you remove. CleanMyMac, of course, would be one of them, and also Sophos (although that is, technically speaking, not a utility). Are there any other programs that you uninstalled? If you have no other third party apps (whether utilities or other kinds of software), then you should be OK. But, if you do, you need to take an inventory of them.
Now, from this:
http://www.everymac.com/systems/app...uo-3.06-21-inch-aluminum-late-2009-specs.html
it looks like the original OS that was on your machine was the "second" version of Snow Leopard, OS 10.6.1. The last version of that OS was 10.6.8. Given that you have upgraded to Sierra, I suspect that the (hidden) Recovery HD partition was created by Sierra. (By the way, what version of Sierra is on the machine now? Apple has issued two updates to the first one, OS 10.12). This link explains how to boot to that partition, and what its capabilities are:
https://support.apple.com/en-us/HT201314
So, what you could do is to boot to that partition, use Disk Utility there to 1) perform Disk First Aid on your internal drive, both at the Volume and Partition levels, 2) assuming 1) said no problems/issues/errors, have Disk Utility Erase and Format (and if necessary, partition (that would be up to you)) that internal drive, 3) do a clean, "virgin" re-installation of the Mac OS (again I would think it would be Sierra), and 4) use Migration Assistant to "migrate"/copy any needed "stuff from your Time Machine backup (you will be offered to do that after the installation of the OS completes). Part of that migration includes admin account setups, password, etc.
Now, here is where I am a little "deficient" about that last piece. I myself keep my Macs "lean and clean", constantly removing stuff I no longer need, and every week, I perform a somewhat comprehensive "script" of disk cleanup/maintenance/repairs, and backups. I also keep all the apps I have up to date. So, when I do that last step, I don't anticipate any "bad" stuff being copied. In your case, though, given there were two Mac OS upgrades done in place, not sure how clean things are. I also use SuperDuper! for my backups, although that should not make much of a difference (except that I can boot my Mac from such a backup).
So, hopefully someone else on here can provide more guidance about your situation.