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Based on those configuration files, I'm surprised at some of the warnings that you're getting. Are you sure that you don't have any stale parameters on the parameter server for some reason? In particular, if you haven't set the "backup_vel" parameter, you really shouldn't get a warning about it being set. Also, you've set the frequency for map updates to 5Hz, but the warning you posted complains about it not hitting 2Hz... something there seems strange. Can you post the output from a "rosparam dump" so that we can see what parameters are actually set?
One thing I did notice, is that you'll probably want to set "static_map" to true and "rolling_window" to false in your global_costmap_params.yaml file if you plan to use AMCL to localize and want to create plans that go across the entire map.
Also, out of curiosity, what version of navigation are you running? What kind of computer are you trying to run things on?
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