Okay so. For some reason things are not lining up where they should be.
My blender setup uses a 45 degree tilted camera pointed at the subject. Between this is a 3200*3200mm plane (scale is needed to get the coords to translate properly, doesn't matter at all for this).
Using a shrinkmap modifier, I can pinpoint verticies on my 3D model, and have them "stick" onto the plane; this results in what should be a pixel-perfect projection of where that vertex is on the sprite.
But it's not. For some reason the coordinates in game do not match and I can't figure out why. Below shows the problem: