LAME is the goto encoder to encode MP3's. Joint stereo isn't a bad thing, it improves overal sound quality, and if done properly you will still have the possibility to hear stuff only left or right, as the artist intended.
There are a lot of frontends for LAME encoding. If you're on a Mac, I suggest XLD, on Windows dBPowerAmp. On Linux you could use the commandline interface to lame, or if you want a GUI SoundConverter
As far as encoding settings go, I usually just prefer V0, they're smaller than the 320s, and have pretty much the same quality.
If I were doing it, I would just copy everything from the FLAC folders to the Opus folders, then convert the files in the Opus folders in place using SoundConverter (it's in the repos). Done.
Here you go. For the future you can use this site to convert audio/video to MP3, I personally use the site to convert mp4s to webms.
For software I use Sound Converter, but it's Linux-only.