Restoration of the CD Rack

Dear Forumites ,

I'd like to ask your opinion about the options available for a small project that I've started recently .
In essence, I bought an old CD rack painted in some strange blue paint. I've managed to remove the paint using orbital sander and some hideous manual labour :)
I believe the timber is pine ( not sure though).

Now to the fun part. The purpose of the project is to stain the timber and to create a traditional Japanese gold leaf painting on top ( my gf is an artist ).

As you can see in the enclosed photos , there are many visible metal brackets and nails in different locations. I've used a wood filler , though it only helped to create a uniform surface . I'd like to stain the CD rack in wallnut/dark oak . My concern is that the stain won't hide all the metal pieces and wood sealer .

Could you please advise what are the options available to create a nice surface finish ?

Thanks in advance
gprp