I found this story a few days ago and just finished reading. It is fun to read, especially the epic battle that followed Burthek's mistake, and also educative. I'm now using grates much more often. I wonder what you're going to do with the clowns in cavern 2. Encasing them in obsidian is a particularly effective and safe method to get rid of them, though you might consider it cheating.
I've tried embarking in an Evil biome once. What I learned was that a butcher's shop should always be accompanied by a tanner, tanning the hide prevents it from reanimating, and a farmer's workshop, to spin the hair or wool, which can also reanimate. I believe that these are the only 2 products of butchering that can reanimate, so while processing them is still risky, you should be safe once finished. So when you butchered the pig in part 14, you could have tanned the hide which would have saved Zulgar's life when she asked for leather and bones. On the other hand, it could also have resulted in the death of your tanner.
The
mysterious cave-in and
dust cloud trees are the result of a
bug that causes trees to collapse occasionally. It has been fixed in v0.40.15. Another quirk of dwarf fortress is that your dwarves can only construct a wall if they have a path to a tile adjacent to it. Hence Burthek was never able to build
this wall. What also might be useful to know is that you can carve fortifications out of constructed walls. However, be aware that
creatures can jump through fortifications. I didn't know that creatures can climb, but apparently they can, which is why
the undead got out of the trap. However, they can only
climb non-smoothed walls, so if you can manage to smooth out the left side of
the pit, you should be able to repair the trap (assuming you did not use constructed walls there).