Great mod. I made the same for the final battle with sahelantropus. Did you notice in most cases 3 files form one theme? There's an intro, middle and outro part for each. The point is that when a battle start a "soft" part of that theme is heard, then the middle action part and when it reaches a critical state, like sahelantropus having low health the outro kicks in.
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The only problem is Alert mode, is too quiet, I can barely hear it, I hope you can fix it in the near future :D