Try turning down the idle. I had a similar problem when I bought my 4Runner. It was idling high and sometimes the rpm's would fluctuate when I pressed on the brakes.

To fix the fluctuating rmp's, you need to turn the idle speed down to about 700rpms and see if that fixes the problem before you start replacing parts you don't need to.

Here's the web page for better detail of the problem if indeed it is your problem. Hope this helps. Good Luck
http://www.geocities.com/toyotashawn/bizzareidle.html