Ctrl-Z is your friend in Lightroom. Slap it like you're playing Space Invaders. If you need more depth-of-field you need to shoot at a higher stop. f/22, f/28 will solve all DOF problems. It will also suck away all light. Tripod. Shutter release cable. You need to get closer to the ground. If you're looking to make those cobblestones pop, get fuckn' on 'em. I've got a Bogen 3221 (that, I realize, is maybe a little older than you are) and one of the coolest things is it's got tripod threads on the bottom of the riser, too... which means you can mount your quick release down there, drop the camera upside down, and literally have it on a tripod half an inch above the ground. 
Yeah, thank god Ctl-Z works everywhere! I was shooting at the highest stop for most the shots - but the really close stones are still not in focus perfectly. Maybe i'm just being picky... Got that tripod and shutter release so all should be good. Scored the good manfrotto stuff, it doesn't do any fancy flips but is pretty solid :)