I want to get rid of manufacturing and install schools. Do I need to somehow re-run the setup wizard? If I do,will that wipe all the updates I have made so far?
No,
Manufacturing is part of the ERPnext App so just hide it via settings/user - show/hide desktop icons.
Same with Schools, You should just hide the school module & Doctypes in the same way.
ok, in looking in more detail I see under setup → Show / Hide Modules that I have manufacturing unchecked and all the options for school checked. What I don’t see is any main menu items for administering or working with all the school document types. I still see manufacturing there, however