Jeff,
I can't really suggest that you be patient, because it's becoming obvious that you have more of that than I could imagine. I can't help but believe it will be worth it when Direwolf is back in your hands, since you already know what you're missing. If they can't find a good solution to the problem, my inclination would probably be to accept the raised finish at the wood-fault-line as the reality of building a bass out of such dissimilar woods, and enjoy it for what it is (a massively wonderful instrument). It may ultimately be a candidate for an oil finish, which would look (and feel) great as well. At any rate, I think we all feel your pain yet envy that you'll get to play this wonderful Alembic again soon enough, and that it will be yours forever.
Best of luck with all of it, Jeff...
John