I'll repeat it again at the risk of being annoying. I would send it back with a list of issues and request a new barrel, timed and aligned correctly that may require a new sight added since this one appears to be out of alignment with a poorly affixed barrel. You are shooting a barrel that is not 100% and can be considered dangerous. You should not have to be working on it yourself.

I do gun smithing myself but if I send a piece away for threading or repair or whatever, I expect it to be done correctly so I can trust shooting it with my life! My eyes, hands and life are important to me, as well as my treasured Krags!

If the request is not accepted easily, I would ask for a refund and find a more reputable gun smith.

If this is the case, please let us all know who this is so none of us will have him do any work for us. Reputations and quality of work, good and bad, should be shared!

Just my 2 cents. Do what you think is best. 

I feel like I'm getting to be an old snot like Dick, but at a much younger age. (Meant to be a compliment, Dick! You've taught me a lot!!)