[Arran]

I usually use some sort of penetrating dye on the junk wood portions, just to darken them up, I only do this to conserve tone spray but it isn't necessary. Oil based stain is useless on anything with a closed grain, you may have noticed that the samples shown in the stores are always on an open grained wood like oak or ash, and even on those it does not work consistently. It's also impossible to hide any areas that have blemishes or have been sanded through, like what your are dealing with.
Regards
Arran