Luckily, it looks like a great many of these errors are coming from items culled by material simplification. I'll go through and comment out the stuff it's not finding and post them as code spoilers here later once I get these cleaned up. I can do that much to help at least.
UPDATE:
Here are the stonesense files to update to eliminate the missing item references, trying to post them as code segments blew past the character limit. I left all of the commented lines in the files so the line numbers should all match for where the comments were inserted to eliminate the previous errors from missing item types. The only one I couldn't track down yet was the 'RABBIT' one, but I'll take that as a challenge.
SECOND UPDATE:
There was a missing </variant> for the 'RABBIT' in caravan_animals.xml. Fixed and re-uploaded. That should fix pretty much everything except some odd file access error for a few of the modified files that does not seem to affect things that I can tell. Note there is no modified artwork with this, but hopefully it'll help as a springing off point for folks that can actually draw.
UPDATE NOTE:
I will try and keep the link to my current progress on this listed here to keep it from getting buried in the post.
Current release (update #7 adding gnomes, orcs and warlocks):
https://www.dropbox.com/s/69yks5fcm1mhxio/modified_stonesense_update_7.7zI just bundled up the entire stonesense directory into a *.7z archive, but here is the list of modified files:
/stonesense/terrain/MaterialWalls.xml
/stonesense/terrain/MaterialFloors.xml
/stonesense/grasses/grasses.xml
/stonesense/vegetation/DT_trees/dt_trees.xml
/stonesense/colors/Colors_Wood.xml
/stonesense/colors/Colors_Grass.xml
/stonesense/colors/Colors_Stone_Layer.xml
/stonesense/colors/Colors_Stone_Mineral.xml
/stonesense/colors/Colors_Stone_Gem.xml
/stonesense/colors/Colors/Stone_Soil.xml
/stonesense/creatures/caravan_animals.xml