Wonderful update and I think I'm going to start using this tile set when I finally completely make the switch to 2010. Good job on compiling the list of different stones, I hope you included this in the download for easy reference.
I might of been a bit abstract with the "weapon looks like scrolls" thing, what I was meant to say is there is a line down the middle of the weapon that makes it look like a scroll (it's a very small detail, yes, but there isn't too many problems I can find with the tile set so I'm listing all I find no matter how small)
Another list of observations:
The remains sprite might have to be tweaked a little bit. It is a little hard to see the detail and can be confused with clothing/armour at first glance, maybe a slightly simpler graphic here.
As for the adventure mode tile set there is the possibility of removing the different varieties of vermin and just use a single tile to save room for other tiles that might be deemed more important.
I haven't played around with the raws for a while but is it possible to remove the Up/down staircase from X? It just a shame to have such beautiful downstairs leading to a X (perhaps the corpse tileset could be used here?).
Also I was worrying a bit about how this would look with the new underground but I have to say it merges great which remains a bigger plus.
I have to stress though that you do find a nice balance between adventure and fortress mode because the environment looks so damn great in both. Chariot's graphic set also seems to match the more realistic environment you have nicely but I've been having problems trying to find a version of his graphic set that doesn't have parts missing (no screenshots for a while).
I'd love to see more input from other people as well I'm not exactly the end authority of design choices.