One really minor issue, I hate to bring it up. The vacbobs are a little tall. They should be about as tall as the marine, but unfortunately are quite a bit taller. I know the heck you went through messing with the shapes patches, so if it's not easy to fix then don't worry about it.
Maybe if you can modify the shapes patch make the height around 85%?
Or would that look funny? maybe the marine can just be short?
[EDIT]I know the official map file had problems with the exploding vacbobs being color table 2. But shouldn't the exploding vacbobs be green not copper for colortable 3? Looks like you did it perfect in the images but got confused in the mml?
I went to colortable 0 ones for the HD Monsters plugin if that was what you meant?