Check page EM-95. Step 20 is the ac compressor install.
That area of the tsrm will go over the install order. You can then branch out to the specific part sections as needed (ac compressor, for instance)
The water line under the intake go to the throttle body. Many people (myself included) run that line straight from intake outlet to inlet again so it bypasses the throttle body. The throttle body doesn't need that line for earn weather driving. Most supra owners here don't drive then in freezing weather.