I have a 99 with manual tranny and limited myself to a 1" body lift. It's actually more like 1.25" but I believe it settles/compresses over time.
I highly recommend Roger Brown's site and his body lifts.
4crawler.com
Read up on his site and do not hesitate to ask him questions. He is extremely knowledgeable about all things Toyota, and probably a lot more too.
Not a bad time to upgrade to the poly body bushings also. Take photos of every single mounting point so there are no surprises if you order those. Mine had some non standard mounts- so I chose not to do the poly bushings and Roger cheerfully and quickly refunded my money on those once returned to him.
You need to anticipate and be aware of all the potential changes, there will be a gap for the front bumper for example, so good time to go ARB and mount it properly to the new height.
Not all 99s had the tall rear coils. 891s are a stiff stiff spring that does not suit everyone's taste. I had them for a few months and was happy to find a T4R member to switch with me. I am running 890s now in back and very happy with them for my needs. The 906 is also a great choice in back for a mild amount of lift.