What I provided to is a compilation of 2GR-FE water pump threads I've found at TN/Lexus/youtube. There may be others. Seems like the 2nd Gen Highlander and 3rd Gen Avalon forums have had the most fish in the pond.
One of the threads I pointed to is a 2008 Highlander water pump job.
You can go to:
and buy a 2 day subscription to factory service manual info. Last time I checked it was $15 for that period of time. Do this if you are not comfortable with the doc I've presented or what others might pass on.
Awhile back I pulled the alternator off my Avalon. It was dead - had it rebuilt locally. On the Avalon forum there were a number of threads that addressed this and just about all had a different procedure provided by the threads OP. I got dizzy trying to draw up a plan and said f--k it. Printed them all out and went after it. There may be slight differences from year to year as far as what has to come off and how you get it out. I'm one of these types that will yank something off even if not specified in the book if it gives me a cleaner shot at something else further down the trail.
Take pics and a lot of notes as you're moving along. Put nuts/bolts/etc in baggies with a slip of paper in each identifying where they go. Arrange parts in chronological order as they are being removed. Helps prevent reinstallation mysteries.