I opened the file in 2.49. The rig still worked, though other problems existed.
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Select mode was disabled in edit mode.
The mesh had no faces, just vertices and edges, I selected all the vertices, pressed F then selected Auto Fill, which worked ok for most the mesh.
Some faces were missing, some were filled incorrectly, so I had to check the mesh, deleting, refilling, and recalculate the normals.
This took some time fix.
Renamed the meshes, h_head, u_torso, l_legs.
Added empty tags and parented them to pose bones, tag_torso, tag_weapon, tag_head.
For a test, I thought it would be best to make a walk animation, then just use that for all animations.
Tried to export, got an error.
md3_export.py, line 317, in FileSelectorCallback, Export(filename)
md3_export.py, line 312, in Export, md3.Save(file)
md3.py, line 539, in Save, self.GetSize()
md3.py, line 487, in GetSize, self.ofsEnd += s.GetSize()
md3.py, line 234, in GetSize, sz += v.GetSize()
AttributeError: 'int' object has no attribute 'GetSize'
I found the error only happened with the legs, so maybe I missed something.
It did save the md3 files, so I tried to test them.
I added the files to a new model\player\folder, I couldnt select the model from the menu, so I guess need to add player info somewhere.
So I tried to overwrite the penguin model, this worked but after selecting the penguin, the model wouldnt show.
I found lower.md3 was 0kb, so I removed this and the head.
I selected the penguin, it came up with an error that the upper.md3 had more than 1000 verts.
This is correct, the body has 1454.
So I tried just the head, this worked, it was a tiny head, and an odd animation, but it did work.
After some messing about, I found it was best to make the player in the z dimensions -25 to +25.
I was able to load the body mesh on to the penguin correctly, I seperated the hands to decrease the vertices.