Yes the order is Mac Pro->Powerd USB Hub->Monitor Hub. As I said I removed the USB connection to the Monitor Hub as I wasn't using it.
Connected to the Powered USB 2 hub is a powered 2TB Western Digital External HDD (for TimeMachine), a bus-powered HP Webcam HD 2300 and a powered Winstars SATA Hard drive USB 2 docking station.
Connected directly to the Mac Pro USB 3 ports is a unbranded bus-powered 500gb USB 3 external HDD (which frequently disconnects itself from the new Mac Pro - it rarely did this when connected to my 2010 Mac Pro), a bus-powered Kingston USB 3 multi-card reader, a wired Apple Keyboard and of course the powered USB 2 hub.
Connected to the Thunderbolt ports is a Caldigit T3 Raid and my 2 monitors via Apple TB to DVI convertors. The second monitor is a Iiyama PL2710HD but unlike the BenQ has always switched on after sleep - the only difference is it never had a USB cable connected for its built-in USB hub.
My wake from sleep procedure is as follows - I press a key on the keyboard and wait about 5 seconds, then type my password and hit enter and wait around 5 seconds, then power on both monitors. Both monitors have came on without any problems in over a week now. My Mac Pro is sleeping from around 6pm each evening until 9am the next morning. At weekends it sleeps a lot longer.
I also have boot up crash issues that I thought were caused by my Caldigit T3 thunderbolt raid, but on testing again last weekend the Mac Pro crash was caused by the bus-powered 500gb USB 3 external HDD! So now I'm totally confused... its not a major issue as I rarely power the Mac Pro down.
A couple of ideas I had suggested to me by various Apple experts was to make sure the monitors are plugged in to different Thunderbolt buses on the Mac Pro. Secondly when performing an OSx update to 10.9.4, download and install the 10.9.4 Combo update instead of using the software update method. The Combo update will re-install, verify and fix all drivers on the Mac Pro. My Mac Pro came with 10.9.1 installed so it automatically installed the 10.9.4 Combo update as I suppose going from 10.9.1 to 10.9.4 required it.