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The warning about missing desired rate is not related to the robot spinning near the goal. You can set the control frequency with "controller_frequency: 9.0" as the very first line in the base_local file. Before the TrajectoryPlannerROS: line. The warning doesn't mean anything is failing. Except for clogging up the screen and log file, that warning is harmless and can be used as diagnostic later when you're optimizing.
Tip 1:
You have min_in_place_vel_theta: 0.4 set pretty high. Try 0.05 for that.
Tip 2:
In you local planner you should try to increase the goal tolerance from default. See this page: http://wiki.ros.org/base_local_planner. This will make it easier for movebase to conclude you've reached the goal. The default for yaw_goal_tolerance is 0.05 so if you have the min theta velocity at 0.4 I can see robot having issue parking at the correct angle. Lower min theta to 0.05 and increase goal tolerance to 0.2 and see if that fixes it. Then retune once it's working
Question 1:
You have holonomic marked as true. Is that really true?
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