In addition, these are no longer touch attacks since you're using arrows to deliver them, so your chances of hitting with each shot probably aren't that great, compared to touch attacks. The damage isn't nearly that high when you take all those factors into account, and it isn't anything classes like Duskblade can't do. I'm more worried about using spells like Irresistible Dance along with it though, but that's 8th level and Mind Affecting so it shouldn't be too bad when you're so high up.
The d12 is mostly for flavor reasons, since dragons get d12 as do dragon disciples. It doesn't really make that much difference besides a little extra HP, so it seems harmless.
Probably not. There are plenty of mystic theurge rewrites on this very board, and I don't feel like I can bring anything new to the table.