I love the idea for your mod, and I agree wholeheartedly about the mutation problems. They just have no place in the game other than for roleplay, and even that only makes sense if you start out as a mutant.
I also love the idea of roleplaying a ninja turtle :)
As for the mod, I tested it for a bit and it has some problems. Armor seems to work fine, as well as books and mutagen, but the mutations and their categories are borked. I tried out Cattle first to see if you changed anything and I couldn't get past threshold no matter how many serums I injected. Also tried tortoise, ursine, beast, raptor and troglobite. Ursine couldn't get past threshold either, raptor did it in just 3 serums, beast took 17 to get to it and troglobite worked as I expected from vanilla, taking some 13 serums. Tortoise has a buttload of mutations, but other than generating a huge number for mutation category strength and me being unsure how to trigger snapping jaw, it seems to be working ok.
Basically what I think is the problem is that the categories for certain mutations that you changed got borked, especially the ones used by tortoise. Regardless of which serums I tried tortoise nearly always was the strongest category, and the other categories sometimes didn't make sense either. For example, after consuming 50 ursine serums, I had insect, raptor and elfa categories at 300ish to 350ish, tortoise was 440 (highest of them all) and ursine a measly 208.
With no mods, ursine took a whopping 31 serums to break threshold, but the category level was the highest at 224, and tied with raptor. Oddly enough, after breaking threshold, lizard and raptor overtook ursine by over 100 points, at over 600 to ursine's 500, which may be a signal that even vanilla mutation categories are borked somewhat. It probably isn't right that Raptor needs 3-4 serums for threshold and bear needs over 30.
Anyways, I think I will like using this mod for a troglobite character, but I wouldn't use it for a beast-like thing yet.