1. Installation is a bit too finicky. On the forum here you should just say "Download the .zip into your trespasser root folder and extract. If you are not using Trespasser CE, then read the readme for further instructions" and have it be that way, rather than forcing us to open the readme and then extract different directories from the zip into different directories in Trespasser. I know this is a minor complaint, but having it the way you've done it gives players doubts as to whether or not they installed in correctly.
I will work on doing a better installation instruction, been stressed out all day so I did a quick one. I didn't focused too much on it since you can just do the same like any other fan level. Also, most people here atm know how to install a fan level (anyone who will probably try this out anyway).
2. The level didn't load the default CE way you had it come with, I had to move the map directly to the data folder and remove the old copy before it would show up.
Which map, and which old copy?
Did you add any new acts to the raptors?
I did not. I believe you enabled some with the .ini file in CE, haven't spend any time on the raptors.
One bug I did see was that the alpha boss raptor spawned but didn't activate until I got closer to it. It was stuck in that spawn pose.
I do not have this issue. Do you have the max activated dinosaurs option set in the .ini file? If that so, try disable it. Also, I played with the settings found in the "trespasser_dx9.ini" example configs folder. No other settings have been tested, as that will take too much time.
1. Fix the blood palette issue (not that important as it still looks gory)
As mention in the readme, I'm aware of the problem, I need to find a palette that works will all terrain textures, since I use textures from both AS and SUM.
2. Fix the alpha raptor's activation distance.
See above.
And optionally:
3. Prevent the player from seeing the alpha raptor when it spawns. Perhaps move the spawn trigger somewhere else.
Because the location is pretty small there is no way to move it so the player don't see her, as she is bigger than the buildings, you can't hide her.
4. Make the way to get out of the boss arena some other physics puzzle besides box stacking (behind the boxes or something so as to hide the alpha raptor from spawning)
As I said. My intention is to combine things from various official sources, not add things I would like to see. I have no intention in doing a remake of the levels. Minor things are added as eye candy (like the shoulder part of the hunter, and the rib etc), but no really changes to puzzles. Also, it's a direct import of the ending box puzzle found in build 96, and it works fine.
I also have no intention in making it possible to hide the alpha raptor, since it's a boss battle, and in build 96, you could only finish the game if you killed the boss. It is meant that you are going to kill the raptors, and then finish the box puzzle.
I might consider redoing some textures to help you with your project...
Then again, I have no intention in doing a remake of any kind, as mention in the Readme. So I will not redo any textures as I will only use what's found within the game files and from official asset. I will not use any fan-made asset for it (unless it's physics made for models not found in-game, like from Mystery Models).