The first thing that you have to do is to force gpus at a specific Powertune level. You won't hurt the cards, you will just draw some more power. Some cards are more efficient the the others at powertune level 0, but when you rise powertune to 10 or 20 the get equal. So, first thing to do is:
"gpu-powertune" : "10,10,10",
see what happens, then try also
"gpu-powertune" : "20,20,20",
And don't be afraid to do some overclocking ... E=1000 and M=1500 should run just fine at 880 kh/s.
Noted, I'll have a play with the powertune some more tonight. I did dabble with it a little early days when setting these rigs up, but decided not to set powertune till I had a reliable baseline.
Regarding E and M, again I did play a little, and I found I could get the XFX cards up around 875-900khash each, but while I wasn't getting any noticeable HW errors etc. I did see the WU value either not really increasing, or perhaps even decreasing a touch. That, combined with a couple of forum threads suggesting the R9 290 struggles to push WU up despite khash increase when you increase these, caused me to leave near stock initially.
Thanks.