The three elongated holes per bearing carrier are the way to adjust ride height. To run the ride height in its lowest position, the bolt should be higher in the elongated slots.
When I lower the ride height, I do it with the kart on the ground. Loosen all nine bolts and the axle will shift to the highest position (lowering the chassis ride height). When raising ride height, place the kart on a stand. Loosen all nine bolts and the axle will drop to the lowest position (raising the chassis ride height).