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All of the yaml files for navigation refer to planning. In your case, all of the laser sources there should reference your Hokuyo.

To use a different laser with AMCL, simply write an amcl launch file which remaps the input laser topic to AMCL to use your laser. You'll probably want to replace default amcl_onmi.launch that comes with amcl with something like:

<launch>
<node pkg="amcl" type="amcl" name="amcl">
  <remap from="scan" to="sick_laser"/> <!-- remap laser input to use your sick laser -->

  <!-- All of the original parameters from amcl_omni.launch -->
  <!-- Publish scans from best pose at a max of 10 Hz -->
  <param name="odom_model_type" value="omni"/>
  <param name="odom_alpha5" value="0.1"/>
  <param name="transform_tolerance" value="0.2" />
  <param name="gui_publish_rate" value="10.0"/>
  <param name="laser_max_beams" value="30"/>
  <param name="min_particles" value="500"/>
  <param name="max_particles" value="5000"/>
  <param name="kld_err" value="0.05"/>
  <param name="kld_z" value="0.99"/>
  <param name="odom_alpha1" value="0.2"/>
  <param name="odom_alpha2" value="0.2"/>
  <!-- translation std dev, m -->
  <param name="odom_alpha3" value="0.8"/>
  <param name="odom_alpha4" value="0.2"/>
  <param name="laser_z_hit" value="0.5"/>
  <param name="laser_z_short" value="0.05"/>
  <param name="laser_z_max" value="0.05"/>
  <param name="laser_z_rand" value="0.5"/>
  <param name="laser_sigma_hit" value="0.2"/>
  <param name="laser_lambda_short" value="0.1"/>
  <param name="laser_lambda_short" value="0.1"/>
  <param name="laser_model_type" value="likelihood_field"/>
  <!-- <param name="laser_model_type" value="beam"/> -->
  <param name="laser_likelihood_max_dist" value="2.0"/>
  <param name="update_min_d" value="0.2"/>
  <param name="update_min_a" value="0.5"/>
  <param name="odom_frame_id" value="odom"/>
  <param name="resample_interval" value="1"/>
  <param name="transform_tolerance" value="0.1"/>
  <param name="recovery_alpha_slow" value="0.0"/>
  <param name="recovery_alpha_fast" value="0.0"/>
</node>
</launch>

Since you're using a much nicer laser than the default parameters expect, you should probably tune the parameters to AMCL to fit your needs.

When adjusting the parameters to AMCL, it's generally best to run AMCL by iteslf (without the rest of the navigation stack) and drive the robot around by hand to test the quality of your localization, before you try to navigate based on your localization.