I turned off quiet mode

What How ?

Can I set startup-sequence to complete one line at a time after a key press or some other way to slow it down?

Add the line

set echo on

to the beginning of the startup-sequence, then each command is listed before execution. Press the space bar or any key to halt the output. Delete the input to continue.

Add something like

ask "press enter to continue"

between LoadWB and EndCLI in startup-sequence in order to automatically halt before the initial Shell window closes.

get a pop up dialog box at what appears is the end of the booting process that goes away rather quickly. It says something like 'Intuition is trying to close an open window.' and something else with the retry and cancel buttons. It goes away by itself. Is this normal? What can be done about it if it isnt normal?

Intuition tries to close and reopen the Workbench screen in order to set the screen mode configured in Prefs/Screenmode. It cannot do this as long as other windows are open on that screen. So while the initial Shell window is open, the requester appears and it disappears automatically when the shell window is closed.

Short: yes, it's normal.

Bye,
Thomas