You won't find many folks running that large of a body lift. Most would rather use some type of suspension lift. A few folks run body lifts 1" or so because of an engine change and need a bit more hood clearance.
Body lifts tend to tear up the Sammi body underneath by poking holes through the mount area. The can be unstable depending on your type of wheeling and yes there is a tip over factor as you raise up and especially on an incline can change the stability triangle within the vehicle.
As you mentioned alot of folks flip the axles... (that is an old school term) or run SPOA lifts (spring over axle). This and your choice of springs can give you adequate lift to run 33's.
YJ / Cj jeep springs and missing link shackles or a RUF (rear samurai springs up front) and relocation plates, missing links or extended shackles will get you there.
There are a boatload of methods to choose from and research is your best friend. Start reading anything and everything about the different type of Samurai lifts and what is required. It will help you tons.
Gearing is a bit similar depending on how you want to wheel. I run 5:12 / 5:13 differential gears and a 6:5:1 transfer gears on 34x9.5x15 TSL's off road and on the road and love em. I don't drive the highway very often. Mostly around town and to play, and I don't rock crawl.
So there is some food for thought to get you started...
By the way we love photos so lets see what you have goin on there....