Unable to move links within URDF file

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Hi!

I'm currently struggling with URDF. The model of the robot is a Kuka KR3 CR. I used a Collada file (from OpenRAVE's collection of robots - Rosen Diankov actually created this model for a previous project of mine :)). There were a couple of problems with it (including partially flipped normals of some of the faces and some of the links (you can see that in the image below - a screenshot from OpenRAVE's visualization tool) have some weird geometry issues:

That's why I used Blender and Meshlab to fix the issues. In order to obtain the separate links I used the collada_to_urdf tool. It extracted an URDF file along with the links (one Collada file per link which I converted to OBJ format). It seems however that the tool doesn't work properly and some of the links are now not where they are supposed to be:

I tried changing those but moveit setup assistant doesn't show the changes for some reason...

The original URDF can be seen below (I replaced values such as 6.1342423e-33 with 0 since those are obviously rounding errors):

 <?xml version="1.0"?>
  <robot name="KR3CR"
     xmlns:xi="http://www.w3.org/2001/XInclude"
     xmlns:gazebo="http://playerstage.sourceforge.net/gazebo/xmlschema/#gz"
     xmlns:model="http://playerstage.sourceforge.net/gazebo/xmlschema/#model"
     xmlns:sensor="http://playerstage.sourceforge.net/gazebo/xmlschema/#sensor"
     xmlns:body="http://playerstage.sourceforge.net/gazebo/xmlschema/#body"
     xmlns:geom="http://playerstage.sourceforge.net/gazebo/xmlschema/#geom"
     xmlns:joint="http://playerstage.sourceforge.net/gazebo/xmlschema/#joint"
     xmlns:interface="http://playerstage.sourceforge.net/gazebo/xmlschema/#interface"
     xmlns:rendering="http://playerstage.sourceforge.net/gazebo/xmlschema/#rendering"
     xmlns:renderable="http://playerstage.sourceforge.net/gazebo/xmlschema/#renderable"
     xmlns:controller="http://playerstage.sourceforge.net/gazebo/xmlschema/#controller"
     xmlns:physics="http://playerstage.sourceforge.net/gazebo/xmlschema/#physics">

  <link name="link1">
    <visual>
      <origin xyz="0 0 0" rpy="0 -0 0"/>
      <geometry>
        <mesh filename="package://urdf_collection/meshes/kr3cr/link_1.obj" scale="1 1 1" />
      </geometry>
    </visual>
    <collision>
      <origin xyz="0 0 0" rpy="0 0 0"/>
      <geometry>
        <mesh filename="package://urdf_collection/meshes/kr3cr/link_1.obj" scale="1 1 1" />
      </geometry>
    </collision>
    <inertial>
      <mass value="1" />
      <origin xyz="0 0 0" rpy="0 -0 0"/>
      <inertia ixx="0.4" ixy="0" ixz="0" iyy="0.4" iyz="0" izz="0.4"/>
    </inertial>
  </link>

  <link name="link2">
    <visual>
      <origin xyz="0 0 0" rpy="3.14159 0 0"/>
      <geometry>
        <mesh filename="package://urdf_collection/meshes/kr3cr/link_2.obj" scale="1 1 1" />
      </geometry>
    </visual>
    <collision>
      <origin xyz="0 0 0" rpy="3.14159 0 0"/>
      <geometry>
        <mesh filename="package://urdf_collection/meshes/kr3cr/link_2.obj" scale="1 1 1" />
      </geometry>
    </collision>
    <inertial>
      <mass value="1" />
      <origin xyz="0 0 0" rpy="0 0 0"/>
      <inertia ixx="0.4" ixy="0" ixz="0" iyy="0.4" iyz="0" izz="0.4"/>
    </inertial>
  </link>

  <link name="link3">
    <visual>
      <origin xyz="0.1 0 -0.35" rpy="1.5708 -0 0"/>
      <geometry>
        <mesh filename="package://urdf_collection/meshes/kr3cr/link_3.obj" scale="1 1 ...