Long shot, but even though your DVI ports are DVI-D, your DisplayPort port should be able to output VGA using a DP->VGA adapter like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16815158150
(First google result)

They're pricey but might be dummy moddable.  I wouldn't RMA your motherboard since it obviously DOES work with a real monitor attached and your boot display set to PCIe (this is correct even for headless operation).  If that doesn't work, I would consider selling your cards (R9 290's are tough to find so you'd probably get more money back selling than if you returned and paid a restocking fee) and buy ones with DVI-I ports that you can easily dummy-plug.