Thank you for the greater details as I now have a better understanding of what you are experiencing.
I am going to suggest a few different remedies though you will have to use your own judgement and stop using if you feel any negative side effects.
I would suggest using a little Hydrogen Peroxide solution (6%) which you can get from the chemist and either put it in the bottle cap and dip each finger end in it or use some cotton wool. This may produce a slight tingling sensation. If it is painful with your symptoms then you will have to decide if you want to continue.
About 15 minutes later I would suggest using some Neem oil for coating the nail fungus and the ends of your fingers and toes: you can do your own search on the search engines for a product, which you feel will help. If did a search and this one sounded OK to me: http://www.ghorganics.com/SupremeNeemOil.html
Then to carry this out about half an hour to an hour before going to bed; this will allow time for the oil to be absorbed by the skin.
If the need oil works you may not need to use the hydrogen Peroxide to kill the fungus first.
The other product you could try is ZetaClear. It is pretty expensive but it's worth every penny.
I feel you should not file your nails too close as it may damage the skin and let the fungus in. I will leave this to your own judgement.
Though I feel the most important part is your own thoughts about the condition. Your own self talk should be positive and supporting if you want to know the effects your thoughts have on your body you may like to get a copy of the DVD titled: "what the bleep" http://www.whatthebleep.com
Anyway let me know how you get on and only follow this advice if you feel it is helpful and not damaging you in any way.