A question for the original post. Are the wagons being hand stacked or stacked with an accumulator?
We have a baler with a kicker but in most cases still stack the wagons to get more on them. Have two flat wagons and a homebuilt kicker wagon. If stacking by hand I recommend putting sides on it especially with hired help who can't stack. Less risk of loosing a part or or a full load as well. Not to mention you can more bales on the wagon.
As for the actual building of the wagons we use 4x10's or 12's for beams lay down tarpaper on the tops of those to prevent rot before laying the bo