The manufacturer recommends running them at around 1/2" clearance on the rears. I had them at around 3/4. Part of the clearance problem for me is the Skyjacker springs. The 6" lift springs travel more than the stockers, and are weaker, too. So yes, at 3/4" I can feel them on even moderate bumps in the road. Maybe not the case with stock or better springs. They're in contact with less than 500lbs. in the bed.
The Timbrens stil work great as an overload spring in my application. I hauled a ton of gravel in the bed with them last year, no problem. But I'll never buy another set of Skyjackers. Maybe some custom springs, or some type of air ride. Skyjackers ride nice, but that's about all they're good for, IMHO.