build a frame, to fit the a frame, just under the frame of the loft area. cover with hardware cloth. remove loft decking, and place hardware frame just under the loft frame, with the hardware cloth on the bottom of the frame.
they can roost on the loft deck frame, the hardware cloth will keep predator proof.
I'd build the nesting box to fit the window on the far end of the tractor. I'd also use a flip top, sloped lid on the box, that you can securely latch closed.
Seems like it would be easier to replace the chicken wire with hardware cloth? I don't know if I could build the frames like you're talking about, mostly because I don't totally understand.
But I really like the nest box idea.