Good job on a beautiful piece of wood.
Like Hannah said, those cracks are repairable with a good carpenters wood glue, a fine tipped paint brush and a little dark stain, and they will look like they belong there, especially since they don't run all the way through to the other side, so it's definitely doable.
As for alignment that also can be redone with some imagination, and some re drilling, which isn't a big deal since it won't be visible after it's done.
You've done some good work, and it would be a shame to give up on it, so keep up the project and let us see how it turns out!