A picture paints a 1000 words..
First - turn your double-width bracket in to a single-slot (cost AUD 25)
This image shows that almost ALL 2.5 width cards can be cleanly installed in SLOT 4 (total clearance above a standard double-slot like the RX480 pictured is 15mm)
..with that said -...
I recently got my new Mac Pro up & running (a Mid 2012), and because in the short term I've moved my hard drives over from my previous Mac Pro (a Mid 2009), I currently have the following installed:
2 x 1TB Hard Drives, configured as a single 2TB volume via RAID 0. This volume is the boot...