All the latest talk about dodgy flashlight apps made me check mine and I found it was on the list of possibly suspect malware.  It was about 12MB in size, which seemed kind of big for a flashlight app, and for the last few months I've noticed a lot more lag on my phone.

I've now replaced that app with a small 73K one, which works just as well, but from what I've read the previous app may have installed a rootkit or something and that might still be installed and running.

So I've decided to restore my S3 back to factory settings.  Not only as a security precaution (I don't have any real evidence that my previous flashlight app was indeed malware) but also just to give it a general clean out.

I know that after the restore I can sign back into my Google account and all my contacts appear and my previously installed apps will be downloaded.  But there are lots of stuff that won't have been backed up by Google, such as all the tweaks in my settings that got things set up just how I like them, numerous little sound files I've downloaded over the years as notifications and ringtones, etc.

My first instinct was to do a full backup via Kies (even though I hate that software as it often bombs out for me) or some other backup software, but then I wondered if this would just back up and restore any malware, making the whole operation pointless?

What do people suggest?

I'm running the stock Android 4.3 and my phone isn't rooted.  I'm quite happy with this and I'm not looking at moving to a custom ROM.

After a factory restore will my phone revert to the version of Android that it originally came with?  So I'll have to download any Android updates again?