I've never done this with my guitars, but I always heard to do it properly, you need to have the proper files and my opinion, not cheap.

/http://www.stewmac.com/shop/Nuts,_saddles/Special_tools_for:_Nuts_and_saddles/Double-edge_Nut_Files.html

There is a debate on what value changing out the nut has. In your case, due to action, there certainly is reason to consider a nut change. Material on the other hand really makes minimal difference other than bone, tusq and some of the harder materials hold up better to wear caused by tuning. Since you are fretting most of the time, the material has little or no impact on tone/sound. The saddle plays a much bigger role in changing tone/sound.

I don't know if you ever used this site, but I found it to be a treasure of information.

http://frets.com/FRETSPages/pagelist.html

If you haven't used or read this site, scroll down to Instrument Setup and check out the two sections regarding guitar nut.

Edit: I see Shiner posted as I was writing (interupted by the Indians game), but some of the same points are made.