Also double check that the planks are centered on the car width. If you are modeling the style with the overhanging deck, you will need to align the shorter boards over the stake pockets by eye. When done, set a metal ruler or other long weight on the deck while the glue sets. Once the deck is dry, some of the boards on the overhanging deck may need trimming to provide full clearance over the stake pockets. Drill out the hub for a three scale foot length of wire, drill the brake wheel mount on the car end to match and mount the wheel.
Most flats have a brake wheel that can be dropped flat on the deck to clear long loads.
One way to protect the fragile wheel if your car is subject to rough handling is to push the brake rod all the way through the mounting until the wheel is flush on top of the deck planking before gluing it in place. If you do this, make sure the bottom of the rod is high enough to clear the track and any crossings or other obstructions. Of course, the AF stake pockets are not hollow so it is difficult to add loads that require stakes.