I just took a look at NBs recipe. I have an all grain recipe that I really like. It adds Brown malt(1lb), a little of the Cherrywood smoked malt(6-8oz), a little honey malt(4oz) and a lot more chocolate malt than their recipe uses. I don't use either the black malt that they use or roast barley. IMO they give too much of a roasty, burnt flavor in this beer.
If I were you, I'd plug their recipe into an online recipe creator (I use and like Brewtoad, but there are many).
Add some more chocolate malt and maybe some honeymalt and see what that does for you. If you think your last version came out too thin, you could add a couple oz. of carapils or melanoidin malt as well. And I agree with your thought about adding the honey late boil. But, I also agree with danny, don't add more than the 1 lb. honey.