It's a pretty straight forward job with a few pesky parts a long the way. There are plenty of threads out there discussing it. Grant it, you may no be going with a lift but I would search in some of the lift install threads. It should be the same concept. In the mean time, I'll see if I can find something specific for ya.
Here ya go..
http://sonoransteel.com/guide.pdf
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'99 Toyota 4Runner LTD - Dual Locked | Geared | Mid-Travel | 35s | Armored