Hi mate,
As you have 3 different graphics card, your cgminer settings should state a different arguments for each card, separated by a ","
Here you only have a "generic" setting for all your cards, and I believe that is why you don't reach their full potential.
Also I would not use afterburner to set the core clock and mem clock, but add them to the .conf (also separated by "," for each card, in order)
"device" : "0-1" specifies, that this one is the setting for Card 0 and 1 aka both R9 280X. Those need the same settings, it does not change the output whether i run one or two cards with this setting. The 290 only needs one gputhreat so it is on another cgminer instanz.