@Angie16hearts With the bantam pen it looks like you could run some 2x4s from the roof over the extended side of the bottom following the same angle, line it with wire and that would give them the extra space. As for the full size pen there's floor space under the nesting boxes that can be utilized, and have you considered extending the runs length or even squaring it up, that'll open up those low sides and give you the option to add more sections, almost modular status.
Attimus
Attimus