As long as the weapon is of masterwork quality, it can be enchanted. If it's not of masterwork wildfire, you can either get/make one that is, or have it unnoticed with the spell Masterwork Transformation. You could pay someone to put a +1 or the flaming quality (+1d6 fire damage) onto it, or if you have the right feats you could do it yourself. Mind you, a weapon needs to be at least +1 before other properties, like flaming, can be added.
All of these things might be beyond the confines of the beginner's box though, I'm not really sure.
Basically, yes but it costs more and more. You pay the difference in cost from what you have to what you want. So if you have a Masterwork sword and you want it to be a +1 sword, then you pay 2,000 gold for someone to make it better (it will also take 2 days to complete; 1 day per 1000 cost).
Now a brand new +2 sword costs 8,000 gold. If you want to upgrade your current +1 sword, you'd pay 8,000 - 2,000 = 6,000 gold (6 days to enchant). If you want to go from +1 straight to +3, it would cost 18,000 - 2,000 = 16,000 gold (and over two weeks).
In terms of special features, like flaming or holy, those have a +X equivalent value. The math remains the same; a +2 sword and a +1 Flaming sword are the same value, and upgrading from a plain +1 sword to either would cost the same. However, a +2 flaming sword is equal to a +3 sword (18,000 gold).
This is all covered in the Magic Weapons and Crafting sections of the rulebook, once you get it.
Everyone's already covered the answers. But yes, this is beyond the scope of the Beginner Box, but the rules for doing it are in the Core Rulebook. :)