I use those poly jounce bumpers too (I think they're made by Prothane). They only compress about an inch for most hits, and they're pretty firm when they do hit. I factor them in partially in my overall travel setup. If you keep the RE bump stops, you can swap out the red poly bumpers with something like Metalcloak's more foamy set, or go back to stock foam.
FWIW, I run a 3.5 lift with 3" bumpstop in front (6 hockey pucks I bought from the local rink lol), 2" metal stops in back with those jounce bumpers (I started with 3" in the back, but kept hitting the poly over minor dips in the road). Even with drag link flip and raised track bar bracket everything clears. This is the best setup for most of the available stock-fit shocks out there. If you run Metalcloak "six-pack" shocks or coilovers, you'll want to start clearancing to take advantage of the improved uptravel (notch frame, upgrade fenders/liners, etc.).
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