Hi stephen, (or is it Stephen?)
There are quite some problems, but there is also parts that are OK.
The mesh doesn’t show any problems, regarding normals or bad polygons, except the eyes should be inspected, there is something wrong.
The joints come obviously not from Cinema 4D, the orientation is off, hence the -90º. IF you export anything, use the Y is up option. Cinema 4D, so far I can tell, can work with all joints axis orientations, but in some cases having them not in Z seemed to have limited some functionality.
The rig from object had keyframes. This might work in certain cases, but in the moment you move the Motion Clips, and there is perhaps a gap, the key frame animation starts to work again. This might show up for a single frame or longer, based on the gab, and can ruin the animation. transfer that animation as well into a clip.
As mentioned above, if you use Animation clips, the hierarchy should not differ. If you have more or less child objects might be not the problem, but if object are inside of the hierarchy where a new joint chain would start, things will be messed up. The example file I got from you have some joint chains for the same object parts in different positions in the hierarchy.
My suggestion: Use the animation clips that you have created, as long they ALL follow the same structure/hierarchy, and copy a joint hierarchy from it. This rig must be free of any keyframes, as it will be used to Bind the Character.. Now the Information will be congruent.
If you have the same hierarchy, but the joints are not a good fit in scale, please explore the Retarget Tag.
As a side note, I know how tempting it is to start with something substantial. But I would explore anything that you will use with a very simplified set up. Just a few joints a cylinder and any procedure that you will use, can be tested quickly.
My best wishes for your project