So you are going 3.5 in the back and what in the front? I'm getting confused on what you have on what but I'm curious to know.
Cool. For me , it's all about tire size, decent clearance and good driving ..and I've got 2 fairly different Rubicons.
The 03 was thought to be lifted 3.5-4" when purchased. It was an old sky jacker short arm lift. I wasn't worried about the springs as much as the horrible bushings, so I kept the springs and rebuilt the rest.
It measures to have 3.5" in the front and 2.5 in the rear bucket to bucket with the hard top on now - this is near level when you factor in the fact they sit 1" down in front stock...and mine is close to being a tad low in back with the hard top on ..so here comes the new 3.5" rear springs. The idea is to get some rake back. I'll always set up a TJ to have 1/2" -1" of rake for cargo.
The 06 had a 2" puck lift and it looked crowded at the wheelwells with the 16's it has that are about 32.5 inches tall, so I did 1.5- 2 inches in front and kept the pucks for 3.5- 4" and 3" in the rear , with no hard top, so it sits level or a skosh high in back, clears the fenders , has stock control arms and no alignment drama.
Both drive great.
I'm basically working from what I had with each, learning and tweaking my set up. The 03 is in the build threads as AndyG's period correct Rubicon and the 06 is in there, it is a Jeep I bought to resale and has turned into the best Rubicon for the money I'll likely ever own..it's different, but really good all around.