Well mal means bad, mauvaise means badly (adjective and adverb).
Meilleur means best, mieux means better (again, adjective and adverb).
Le copain/la copine more or less means boyfriend, but can just mean good friend in some situations and to some people, but is used more often the petit ami, I find.
People just say le bus for the bus, more or less.
Le jour just means the day, but if you want to say 'have a nice day' you say 'bonne journee' and it changes to feminine. It means more like daytime, whereas jour just means day.
You can just use both conducteur and chauffeur in my experience, might depend on where you are as some regions might use these differently.
I think norriture is more popular but I certainly hear both used. Again, just kind of two ways of saying the same thing.
Libre means free in the sense that 'I am free tonight', and gratuit is used to mean free in shops, i.e. something you don't pay for.
Amusant and drole are basically just amusing and funny in English. Two words that means essentially the same thing.
Super is great, can also be an adverb. Never really heard people use extra, but could be a regional thing. I think you would rather say 'top'.
Content and hereux are pretty much the same thing.
For job I think you would rather say 'le travail', or 'le boulot' but that's a bit slang, kind of informal. le emploi means employment, and metier means profession rather than just a job.
L'instant and le moment mean the same thing pretty much.
I hear people say stylo more often but I guess both are used.
Chambre is more like a bedroom, whereas salle is not. Salle de bains, salle d'eau etc. are fine but you couldn't say chambre a manger.
Le magasin just means shop, and you can use la boutique but they're not exactly the same. I can't quite describe it, maybe somebody else can help.
'Je suis desole' means I am sorry, but pardon is more casual. Like if you want to get past somebody, or you bump into somebody, or whatever, you would just say pardon whereas in English you could say sorry, but in French desole is reserved for apologies.
Montrer is the verb 'to show', so like to present something to somebody or like 'come and I'll show you my books'. Se voir is like to see eachother, so you could say 'on se voit le dimanche', or 'je me vois dans le miroir.'
L'an vs l'annee is a tricky one to explain. Check out this guide, it seems to explain it well: http://www.french-linguistics.co.uk/grammar/when_to_use_an_annee.shtml
I hope that was thorough enough. If I got anything wrong or anybody wants to add anything then please feel free. Just remember that while most of the things you listed are different, some are just kind of usage things which can depend on people and places and things like that.