I have 2 4Runners, 2004 V8 Limited and 2007 V6 Limited. The 2007 recently threw up the battery light on the dash. I looked it up and it refers to an issue with the charging system. A little more research on this site and it pointed to the alternator. I have one of those USB chargers that fits into the lighter plug that displays the voltage. The voltage at the lighter plug was 11.6 volts. I used a multimeter to check the battery with the engine off. It was 11.7 volts. I started the engine and checked the battery again. It was 11.1 volts. All pointing to the alternator.
So I researched how to replace the alternator and found this video. It's pretty useful.
YouTube:
How to Replace the Alternator on a 2002-2009 Toyota 4Runner with 4.0L Engine
The authors website:
How to Replace the Alternator on a 2002-2009 Toyota 4Runner with 4.0L Engine
I also went ahead and replaced the serpentine belt while I was in there. I purchased a
Remanufactured Denso (part# 2100611) from RockAuto for $110.79 ($189.79 - $79 core exchange). I purchased an
ACDELCO (part# 7K834) belt from there also ($24.79).
A few more things. I did all the work from the top of the engine. I ended up removing the engine cover, the battery, battery tray and the fan. All were very easy to remove and gave me some wiggle room for my arms and the alternator.