Since you are going to be hiding the wood that the wire is currently stapled to, it really is more a matter of not splitting that wood. I use an old thin blade (flat type) screwdriver and a hammer to lift staples enough to grab them with pliers, then it is pretty easy to use a rolling motion of the pliers to pull the staples. If the wire is set into a channel (grove) then you may not be able to remove it with out dismantling it at least part way so you can slide the panels of wire out then put the frame back together.
As far as a color to contrast and look good with what you have. I think a hunter green, barn red, would contrast well with the wood you already have.
when installing T&G, start at the bottom and work your way up. I use a special construction adhesive, F-26, but you can also use liquid nails or sika construction adhesive and you can nail or screw, I always use screws when ever possible.
For sealing new wood I like to use shellac thinned with denatured alcohol in a ratio of 3:1, this will seal the pores in the wood so stains will be more uniform in coloration. This same formulation works well if you want to paint new wood too.