Update:

Tried with a stock horse, and re-used the tail bones to make a chariot pole.wheel setup. This worked fine, and would be great with a single rider on the chariot.

The stock animations, though, flap the tail around like a crazy thing. I need to have the chariot wheel a seperate bone so I can animate the wheels, or I would just attach the chariot to the root of the model.

Trying to change the animations now, but the animerge only seems to work one way. I can turn the modified MS3D into a mesh fine, using the mesh converter.

What I can't do is get the animations to work. I can merge the MS3D with the cas animation file, and load the result up into Milkshape. Then I tried to remove all the keyframing on the chariot part, so it remained still. This was fine...but I cannot turn this back into a CAS file. The animation utilities just don't do it.

I have not got any NEW bones... just some in new places.

Frustratingly, I have no idea why these things are not working