Re: full lower supers but not filling honey super
With drawn fames above the excluder there should be no problem. I would say your flows have slowed down enough they aren't bringing in any more than what's needed for the reduced brood production at this time (they reduce brood production this time of year and concentrate on packing honey in around the reduced nest). If they get more flow starting up for fall then they'll start storing above the excluder. One thing you've not mentioned is what sizes are all your boxes? If they are all the same size, then you can try moving a nectar frame above the excluder, but I really don't think it's needed, it's more an issue of the time of year with reduced flows at the moment.
20+ years, raise my own queens, feed when needed, I treat but have not perfected varroa management yet.