For what it's worth the stock LCA setup has them horizontal when neutral or smooth road cruising. The relocation brackets in lower holes will make them lower in the back rear mount than the front chassis mount. With the stock horizontal setup when you hit a bump and compress rear springs the initial movement and forces of rear mount is purely vertical into the springs. When the angled LCA with relocation brackets hits the same bump it transmits forces upwards and slightly forwards into the front chassis mount. Perhaps what you are feeling is a whiplash type of jerk rather than vertical harshness.
