Hi there,
If you want, I can take a look at the files for you. I'll fix the issues, but I'll also write up for you what was done wrong and how to go about fixing it.
I'll need the skeleton.nif, creature's mesh nif, and the animation(s).
Firstly, though:"The following controlled nodes were not found in the nif:"
"Scene Root.00"
....you should only have a Scene Root node and not a "Scene Root.00" node in your skeleton nif and creature's mesh nif ( which should be NiNode 0 - at very top of Nifskope screen). You should have neither referenced in the kf.
As for the twisting around the Pelvis area - this sounds like an animation issue, in the kf itself. I'd attach the mesh to the skeleton nif, and then import the animation that causes the rotation issue. Then, I'd go into the NiControllerManager and to the NiControllerSequence for the animation data, and in Controlled Blocks under "Block Details" of the NiControllerSequence, expand it and see which "NiTransformInterpolator" goes to the Pelvis bone - make note of which interpolator this is. Then, expand NiControllerSequence until the NiTransformInterpolators and NiTransformDatas are seen. Go to the interpolator for the Pelvis, then go to the NiTransformData under it, and in the NiTranformData, expand the rotation data. Play around with the rotation values until the mesh is rotated to not be twisted, while the animation is at timeframe 0 of the animation (if twisting begins at that timeframe, else go to timeframe where twisting begins). Under XYZ rotation data, every 1.5780 value is roughly a 90 degree rotation. Double that number is a 180 degree rotation, etc. Then, when you've gotten the right values where the mesh is untwisted, enter the same values in the kf-only nif for same bone's NiTransformData.
Of course, you could fix the anim in Blender or whatever program you used, then export it again so that you don't have to do the Nifskopery. But I don't use Blender, so I offer the info above, in case it's needed.
Koniption