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Alright, your mod is finished and ready to be exported back into the game. Our goal with exporting from Blender is this:

1. Select objects to be exported
2. Apply all the custom shape keys you may wish to apply
3. Apply all the modifiers (except Armature)
4. Don't lose any of the special shp_XXX shape keys
5. Triangulate the mesh

Start with going into object mode and hiding all the objects you don't want to be exported

Then press File > Export > FBX

Turn on the checkbox to export only Visible Objects.
Also check the Apply Modifiers and Triangulate Faces boxes.

And if your mod didn't have any Shape Keys along with Modifiers you should be good to go.

Because Blender is too dumb to apply modifiers to objects with shape keys.

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Another weird issue is that TexTools tries to apply all the non-special shape keys on import and I think does a bad job at it, keeping normals from basis when it does. I'm not entirely sure, but if you can help it apply what you need while in Blender.

[WARN] Group: 3 Part: 0 :: 391 Vertices had major corrections made to their weight data.
Harmless, means model weights aren't normalized (sum of influences of certain vertices exceeds 1), gets fixed by TexTools I think.

[WARN] Warning: Mesh: XXX Part 0.0 - Does not have a valid skin element. This will cause animation issues if this is intended to be an animated mesh.
Object doesn't have correct skeleton assigned to it in the Armature modifier

[WARN] Critical Error: FBX is not fully triangulated. Please export from your 3D modeling program with Triangulate option enabled.
As it says, all models gotta be triangulated.