To get 290x with dual monitors / multi monitors (works with 3 for me) boot with one monitor, put computer to sleep, then plug in 2nd monitor (or 2nd and 3rd), then wake the computer, profit.
I have a 290x on Yosemite using Clover with an x79 board. I found this out after hours of troubleshooting. The only thing I changed in the config.plist was to use Hawaii framebuffer, and if you have a problem with dual monitors then you probably don't have to worry about this since I have the same problem as everyone else. Tonight I will experiment with a script to put the computer to sleep at bootup to see if having 3 monitors connected will work after sleep and wake, or if OS X has to boot with only one monitor. This answer will come soon since I am on my way home now. The script was from the old 7970 days when a sleep trick was the fix for that. I will post the source for this and instructions on my next post.