We'll do the easy ones first:
- The death pit seems to be working okay for me.
- The reason your water isn't blue is that your tags are incorrect: your FOF (i.e. water) control linedef and the sector inside the map where the water is to appear should have the same tag (which they currently do); also, your colourmap control linedef and your FOF control sector should have the same tag (but different from the last one).
Your other problems are due to broken sector references. Hover over your starting sector and you'll see what I mean: not all of the linedefs in the loop around your sector light up. This is because it doesn't realise that the non-highlighted lines belong to your sector.
If you switch into lines mode and hover over the ones that didn't light up, you'll notice that the front sector it reports is wrong. To fix it, edit the linedef and change the sector reference to the correct one. You have this problem in a lot of your sectors, not just in the starting one.
The next point is how to stop this happening in the first place. Three rules: never delete anything, never drag one sector into another, and when you're drawing lines, always complete a loop. If you're using WadAuthor, the problems are even more severe, but I forget exactly when they arise.
The restriction on deleting seems a little severe. However, the way to work around it is to make judicious use of the 'merge sector' function, and to drag adjacent vertices on top of one another, as the occasion suggests.
This problem affects enough people at one time or another that it should probably be explained in the Wiki. I might make a start on that shortly.
One last thing: your thok barrier's floor and ceiling should be at the same height, which they currently are not. Otherwise, you can walk into the sector itself, which is not what you want.
