You could probably get away with less boxes if that would allow more room in the coop. Or perhaps even make some external boxes on the side of the coop.
The new dimensions should work for your 4.Ventilation is always key. 1 sq.ft. of ventilation per chicken is a good rule of thumb. The ventilation will need to be as high up as possible above the roost bars so they are not in a draft situation in the winter. What are you doing for nest boxes?
If you include a general location in your profile it really helps.
The coop and run are too small for 4 full size birds. It is a big deal for them to have room when they sleep. I'd guess that they are too crowded and hot in the coop and they are roosting where they are more comfortable. It's...