"We had talked about the dowels but I think a mix of putty after I stain made to match the general color will work better. The holes have allready been filled and are secure. The problem with dowels is that the end grain that is exposed is not very capable of absorbing the stain like the surrounding veneer."
Well when I said dowels I meant using the dowels you get from using a hollow dowel cutter and taking the dowel out of the flat grain. It works really well, especially if the original veneer is thick enough so that you can blend them in without fear or going through.
Just a thought... I am sure based on your previously posted pics they will look great.