I work for a Lexus dealer and $500.00 is about right. My dealer would run $575.00. I would ask then to clean out the screen on the rack and pinion with the install.
The front diff/transfer case has a total of 3 plugs. The one in the middle (from top to bottom) is the fill plug. The one on the top can be used to fill but the middle one is the level the gl5 should be at.
Remove the throttle body and see if any light comes throught the plate. You should have a slight amount of gap between the throttle plate and the body. I'm sure it's got some build-up blocking airflow.
Sounds like electrical feedback into the combo meter due to a possible broken wire along the trunk hinge taillight harness. Cut open the harness around the area that the wires flex when the trunk opens/closes.
Check the blower motor linear controller. Close to the firewall, between the blwer motor box and the firewall. Black color, with a thick wires in the connector.
Easy repair. Lower the engine crossmember and remove the trans crossmember. Remove the right cat and you can see the upper mounting blots for the EGR pipe where it bolts to the water bypass. You'll need some good 12mm swivel sockets and long extension. With an hours time you can replace the pipe.
Unscrew the bezel and fully extend the mast. Then have someone turn off the radio and hold the mast from going down. After 2-3 seconds of pulling on the past, have someone turn on the radio and pull hard on the mast. It'll come out all the way.
I'm sure your evaporator is fine. Check your high and low pressures when it fails to cool. If the low side drops into a vacuum, your expasion valve is stuck. Common on 1994-1996 Es300's
1997-2001 the blower controller is next the the gas pedal. Pull down the carpet and you'll see a connector next to the cabin filter door. You will have to unbolt the gas pedal from the firewall to remove the contoller out of the evaporater case.