It will get better, just keep at it. Try not to worry about it too much, you're doing what you can to fix the problem, so it will eventually get better.
I'd look into putting the additional roosts at the same height as the favorite roost - basically you want all the roosts the same height or it causes fights due to pecking order, and you need enough space between the roosts so that the girls can't reach each other from another roost (to prevent pecking). Give them at least 12" of roost length per chicken, so each chicken has a foot of room along the roost. More is better. This will help reduce stress and pecking order arguments.
Giving them more space will do wonders for them and you, I think. At least 15 square feet per chicken of total space within both the run and coop (minimum 4 sq ft /chicken in coop and minimum 10 sq ft per chicken in run). I think the clutter will help also.
I had a rooster that was almost twice the size as some of my girls - they were 3 ish pounds and he was about 6-7 lbs. It wasn't much of an issue until the first winter (they were all born in April) when the girls started getting feather damage due to mating, but I keep mine confined all the time, so I think that also contributed to it. I bought Down Under Outdoors chicken saddles with shoulder pads, and they've been great. As long as your rooster is nice to the girls, it could work out fine with that size difference.
ETA: If your littles have to sleep in the run for a few months while you work on expanding the coop, that should be okay in a predator proof run. Just make them some long perches to roost on at night. Chickens can be fine in temps down to -20F or -30F, so being outside over the summer/fall where you are at should be fine. Mine live in a predator proof covered run (no coop) year round, and did fine in -9F temps this winter. I'm in north Alabama.