To remove the stains:
A little baking soda and water with a stiff bristled scrub brush will work well. Those of us with soft tops have been doing this for years.
Once you get the stains off, use either 303 Protectant or some Back to Black.
His: '00 WJ 4.7 Limited- Zone 4" SA lift, JKS BPE's
Hers: '03 WJ 4.7 Laredo- IRO 3", 245/75/16 Duratracs, Bilstein Shocks, JKS TB w/KOR Bushings, Rusty's A-Arm Spacer, CORE4x4 Adjustable Front Control Arms, Dynomax Exhaust, RB1 Nav -Coming Soon- Overland Rock Rails