If the errors in the models are simply due to placement, then it's best to correct the error properly with Makou reactor and Ochu (change the coords). I'm not sure if that's the case here.
Do you have a screenshot?
It's not. The new models are obviously taller, so the animation places them inside the ground. This looks very stupid on some fields, because you'd have a character's foot sticking out from under a background layer or something equally ridiculous. Therefore, each and every animation needs to be adjusted to place the skeleton root at the proper height, so that not even a pixel goes inside the ground plane.
The problem is, some animations have been adjusted for the new models, and the majority aren't. This is why there are models bouncing up and down when they're switching anims.
As for Hojo's case, I'm pretty sure I have posted an archive in the past that has the corrected animations?