I found a wee issue with the script, and also solved it for you.
When the script imports an .md5mesh, it applies joint rotations as transforms. Technically, they're supposed to be joint orientations
. When you reexport that model back to Doom3, it all works out the same way, so there's no harm done. The problem is that if you import just the base model in its IK pose, it's unriggable because the joints all have rotation transforms on them, and orientations aligned with the Maya world axis, when it should be vice versa. If you've tried to rig in Maya on a skeleton with rotations on the joints you know the true meaning of futility
Line 773 should change from
setAttr -type float3 ($currentJointName[$i] + ".rotateAxis") $rotation $rotation $rotation;
rotate -r -ws $rotation $rotation $rotation ($currentJointName[$i] + ".rotateAxis");
(That should be a setAttr command but that doesn't seem to properly set the joint's local/object spaces to the rotation axis, making it hard to rig the wrists, among other things - a rotate does the same thing but forces the OS/RS along with)
This imports the model with zero'd rotations and joint axes that are aligned the same way as they are in Doom3 with "r_showskel 1". Thus, you can rig the IK pose however you want to create your own animations, and they export back to Doom3 just fine.
Other than that it's the greatest thing since sliced cheese and I thank you a thousand times.