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All the problems seem to have one thing in common: tf. For disclosure I use ROS extensively but not ROS 2. I base my opinion based on what I've seen on ROS.

1. slam_toolbox cannot register the Lidar. It is unclear if the tf tree is complete, in particular, at the launch of slam_toolbox. Try running ros2 run tf2_ros tf2_echo odom scan_link or ros2 run tqt_tf_tree rqt_tf_tree to view the entire tf tree and see if there are any breaks (requires install).

2. Sometimes, problem 1 does not occur, but "Robot is out of bounds of the costmap!" This is quite straight forward. It just says that the robot is currently not in a free region in the costmap, in particular the obstacle_layer for /scan, and hence is unable to use raytracing to clear or mark obstacles. Moving the initial pose to an free area should fix this.

3. nav2 can't get past controller server! Not sure, maybe controller waiting for initial tf as well?

4. nav2 just sits there timing out waiting for transforms forever! Seems like the tf are being published at rates of 1Hz or more. If you want to use them at this rate be sure to increase the transform tolerances (timeout) in the respective nodes... if they are supposed to publish at higher update rates do check what could be throttling them. rqt_tf_tree might help with idenfying slow updating tf.

5. nav2 drops the "scan_link" for unknown reason forever! Similar to 1. Should find out if there is any break in the tf tree, or maybe slow update rates like in 4. that is causing the timeouts to be reported.