I understand disappointment... it happens. As a dealer I have purchased over 1000 guitars from individual luthiers-- so this is more common than one would hope. Since in my case, returning a guitar to Spain costs more than addressing these issues, I have a luthier who I keep busier than I would like, but do so because I know what it is like to open a case and be disappointed. Even when I send out a "perfect" guitar, tastes matter and one doesn't always make a love match... so we have a return policy. This is something perhaps you might explore with your luthier. (As a general matter, one should understand the luthier's policies on returns, guarantees, flaws in materials or workmanship etc). Ordering from a luthier sight unseen is difficult. In my case, I have know each one well, and have a good idea what to expect. When an issue does arise, they are pretty good about repaying my costs. From what you describe, I would expect him to address these issues, not only at no costs to you, but with no shipping costs either, and perhaps even a gesture on price to compensate you for your pains.
James, Zavaleta's La Casa de Guitarras