I override the crown and scepter in my overrides which I've taken a break on.
http://www.bay12forums.com/smf/index.php?topic=129219.120. Bottom of the page, I saw you wrote in the twbt thread that you were already looking at that though so you should have already seen that. The raws used are different though so maybe you aren't seeing it. (I'll check to see why the crown and scepter aren't working I could have sworn they were) Well they worked for me I just disabled them from the finished good stockpiles they were in to see if they were working. It could be something Toady did that changed it or a feature in twbt that changed? I checked on 40.15 so idk.
All I did to test that stuff quickly was give myself a bunch of embark points so I could get a bunch of items move them all to a stockpile and see if they were overrode, or start with extra dwarves so testing was quicker but yeah if you have a more advanced fort it is much easier to test things.
For the Stoneboulder try these, different tile names depending on the rock type after all
[OVERRIDE:236:T:StoneBoulder:3:32]
[OVERRIDE:236:T:FeatureBoulder:3:32]
[OVERRIDE:236:T:MineralBoulder:3:32]
Instead of the :3: for the tileset name you can use an the actual name of the tileset (without the .png I think, especially when you use more than a few extra ones it becomes more manageable, I didn't do it because that was a feature that came to be after I learned the first way. It makes it easier to manage and understand what that is for from the outside at least.
Really looking forward to how this turns out it's looking really nice so far. I'm no artist and just comparing your work to what I see of my overrides lol..