(I did the messing with the Skill System release from the GitHub)
It looks like you tried to comment out the table installer too. Don't do that. The skill system needs some tables to work (namely all the tables whose names are referred by the error you posted).
I just commented out
#include "Events/World Map Events Installer.event" &
#include "Maps/Master Map Installer.event" from
ROM Buildfile.event, ran
MAKE HACK_full.bat, and the whole thing assembled without issues (both with EA 11.0 & 11.1, for the record, even if some warnings were raised by 11.1). The game itself kinda broke on me (blame the tables that were leftover from circles' older project(s)), but after removing the Class, Char, Item & Chapter Data tables, it ran fine (except for the part where story text is broken since it's replaced by Skill Descriptions and what not, this is basically a non issue if you're making a full custom hack, since you'd replace those anyway).