Since the coop is too small and there isn't enough roosting space it seems that the rooster is reserving the best places for his favorite hens.
The usual recommendations for space per adult, standard-sized bird are:
4 square feet in the coop
10 square feet in the run
1 linear foot on the perch
1 square foot of permanent, 24/7/365 ventilation
If you show us photos of your coop and run and let us know your general location (best to put it in your profile), we can help you make adjustments to your setup so that everyone will be happy and healthy.