I've loaded your save and encountered periodic slowdowns you describe, but they were not nearly as severe as in you case (several seconds max). Dodgy scripting maybe since these enemies weren't going anywhere and apparently the script was trying to find a way for them somewhere. Anyway, i've mopped them up and mission ended, here's the save after the battle if you need it.
CTDs are usually caused by running out of free video RAM. Try turn Compatibility mode option ON and Keep strategy map textures in memory OFF in games settings (strategy map textures are huge). I have all graphics settings on max, but i would turn high detail landscape and sky off in case of CTDs.
Another less likely CTD cause is a corrupted save or autosave (if the game crashed while creating it). Such save would crash when you load it.
Also, try deleting *.bin files in Maps folder subfolders, they are created when you load the map first time and theoretically can also be corrupted. Just delete all folders in Maps folder except _SpeedTree.
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