Re: full lower supers but not filling honey super
Leave the excluder in and move a couple of frames of brood up and nurse bees will move up to look after the brood.
Otherwise there is a very good probability that you will get patches of brood on the honey frames. You probably can't think about harvesting much honey this year as winter is coming.
For next year, if you you have brood throughout the honey frames, you can't harvest until brood is emerged which is late in the season. And honey will be stained by having brood previously in the cells. Try using the excluder.
Also try a top entrance and get bees accustomed to entering from the top from the get go in the spring. Worked well for me, but I did leave the bottom entrance slightly open and as bees are now using the bottom entrance more than the top entrance.
If you always do what you always did, you'll always get what you always got!