As far as beehives go, get enders radius mode on and look to make sure your hives cover all of your growing crops.
viewtopic.php?f=27&t=14575&hilit=modified+by+enderHives that overlap cannot share food, it goes to one or the other. 1 hive or 2 hives sitting side by side will produce the same amount of honey/wax, just divided between the two hives. Hives that don't overlap a crop can't receive "food" from it when it grows. The quality of the products is hard capped by crop quality, soft capped by hive quality. Looking at your screen shot I'd say the south eastern edge of your fields aren't properly covered.
Also, since wax/honey production is purely based on crop growth speed, carrots by far win as the biggest producers if harvested frequently and replanted. They also gain quality the fastest because of this. A true wax farm would be 2-4 hives sitting in a cluster surrounded by nothing but carrots. They would be harvested and replanted for quality, the rest thrown out. 2-4 hives because with that much growth you'd have to be wary of hitting the hive storage cap of 1.0L of honey and 5 wax. Since you're throwing out most of the crop, you could use a scythe and not even worry about storage. Not only would this produce staggering amounts of honey/wax, but your carrot crop would rapidly climb in quality as long as you can afford the LP for the farming skill.