Well, one thing to do would be to look at some of the project vehicles in the Pirate4x4 Toyota board. They recently made a stickied thread of all the project buildups there.
Project Blu does a really nice lift/flat belly.
Rick's quasimoto build is also nice. (same guys that build Blu)
Really, you need to figure out how high you want to go, and what you want to do with the crossmember for the t-case.
Most people I have seen don't even bother messing with the engine mounts, they'll rotate just fine to accomodate the rear lift.
So its basically raising the T-case mounts to as high as you want to go. If you want to go full flat belly, then you'll need to clearance the floor, I believe.
Right now, I'm running a front range offroad t-case center section, with arms I built for it. I can raise it with additonal spacers under the ends. But I'm going to redo the mount to look like the one in rick's quasimoto build. my expereince with the FROR style, is that will the bushings at the frame end, I get a lot of vibration(although it helps control drivetrain torque quite well).
Hmm, actually I bet I know the write up you saw.. http://www.4x4wire.com/toyota/tech/drivetrain_lift/