KISS
99 TJ.
Run a combination of simple low lifts.
Simple 2" lift with either springs or spacers. 1.25" body lift. Combo provides enough room for 35's on my 97 TJ. I'm also using Rubi LJ coils in addition to the spacers. Some say its another 1" lift, but been wheeling for 6 yrs this way. Most spacer lifts include shocks and the rear track bar riser bracket. My lift consists of the ACOS up front to match the rear lift. Rear is the spacer lift. Tera control arms and RE track bars. I use shocks for 6" lift. To maintain my shocks, I have to run longer bump stops and risers to keep the shocks from bottoming out. I use YJ front brake lines along with JKS quick disconnects for the front sway bar. I do have lots of axle walk but I know that. I still have the stock trans skid plate with the 1" motor mount lift, use the stock rear ds, and have the stock rear brake line.
If you want to gain articulation, you'll need more mods, simple but additional. Motor mounts, adjustable/articulating control arms and track bars, front sway bar disconnect/swap, longer front brake lines, and longer bump stops/bump stop risers.
Maintain minimal driveline vibes with a 1" motor mount lift. Consider this, when you lower the trans case skid, you are lowering the back end mount of the driveline, this in turn angles the driveline to help minimize the driveline vibes. Why not lift the front mount 1" higher to get similar tilt and results?
Adding articulating control arms and track bars are necessary as the stamped steel stock components can't handle the forces when articulating with the larger tires and most of the time, the stock rubber bushings won't last. If you can't afford all at once, you can take steps for the control arms and track bars. Add an adjustable track bar in the front, lower front control arm to adjust the front geometry, the upper rear control arm to adjust the pinion angle. In time, replace the lower rear and upper front control arms, and lastly, the rear track bar. You need to keep an eye on the stock components for stress fractures, otherwise, they break. The riser bracket for the rear track bar is necessary to realign the axle under the frame. The front track bar (stock) can be relocated with a bracket, or a hole can be drilled in the axle bracket. Installing an adjustable/articulating track bars is best.
When you start to articulate, depending on the shock length, you will need to replace the stock front brake lines. On the TJ, they will come up short, especially with the front sway bar disconnected. YJ brake lines work well, but that depends on the shock length at full droop. IFS GM front brake lines are even longer and bolt in. The rear brake line you won't need to touch as its the length of the upper rear control arm. Lengthen that arm, you need to address the rear brake line.
Based on the shocks you choose, you need to address the full compression. Keeping the tires off the body as well as keeping the shock from full compression. Longer bump stops are available as well as risers which are secured to the axle housing. THe stock rubber bump stop usually is deteriorated or its gone. Rubber and polyurethane bump stops are available. Aluminum discs are adjustable risers or get the solid riser.