What I noticed from the previous work is they did not differentiate between using the 8mm or 5mm on the thin side. They did position the shaft to be roughly flush with the thin side. So it looks like the shafts did not slip. When I reinstalled the 6 cyl rocker I used a torque of 16 ft-lbs. Turns out thats significantly tighter than the other rockers. That is likely the reason for the leaks. If the orientation of the pinch bolt is insignificant, I might tighten them down and call it good. Any thoughts?

The orientation of the pinch bolts is only significant at the outer cylinders, where the outboard access is limited. You never want to turn the 8mm end. It should only be held in place while the 5mm side is tightened down. For this reason, for the shafts used on the outer cylinders 1,3,4,6 put the 8mm side of the pinch bolt facing away from the #2 or #5 cylinder. This should allow sufficient access for the 5mm allen inboard.