Agus,
Dark Mark has given some sage advice. I've never seen holes drilled that woefully before, and it wont ruin the function of the build but it will ruin the aesthetics.

You are much better off plugging the holes and re drilling them in line, then gluing a nice veneer over the front of the headstock, you wont need it on the back as the tuners will over the doweling.

Also very very sage advice regarding the veneer. its extremely thin and very easy to sand through. If you do that it will be a paint job.

I usually check the veneer for glue spots by using a rag and some gum turpentine. If you see some glue spots and you intend to stain it, you'll need to attack these first before staining and without sanding through.