Hi again,
Sorry, got distracted away from keys for a day or two, but I just updated and tried my 
setup.pl again, and _almost_ all my errors went away with the recent changes to Reconciliation.sql. (Yay!)
The main one that is still shows up repeatedly looks like this:
  psql:/tmp/ledgersmb/lsmb_roles.sql:635: ERROR:  insert or update on table "menu_acl" violates foreign key constraint "menu_acl_node_id_fkey"
  DETAIL:  Key (node_id)=(17) is not present in table "menu_node".
  psql:/tmp/ledgersmb/lsmb_roles.sql:637: ERROR:  insert or update on table "menu_acl" violates foreign key constraint "menu_acl_node_id_fkey"
  DETAIL:  Key (node_id)=(18) is not present in table "menu_node".
Which seems a little weird, I'm no SQL expert but menu_node and menu_acl in my database both have the same foreign key definition for "menu_acl_node_id_fkey":  "FOREIGN KEY (node_id) REFERENCES menu_node(id)".  Unless it's trying to refer to the entire string "(node_id)=(17)" as a key(??)
Also, my dblog concludes with this error, I don't know if it's related to the other one or an independent problem:
  psql:/tmp/ledgersmb/lsmb_roles.sql:1651: ERROR:  syntax error at or near "END"
  LINE 10:    END IF;
            ^
  psql:/tmp/ledgersmb/lsmb_roles.sql:1655: ERROR:  function tg_enforce_perms_eclass() does not exist 
  psql:/tmp/ledgersmb/lsmb_roles.sql:1659: ERROR:  function tg_enforce_perms_eclass() does not exist