Sadly, customized PCB designs from manufacturers are often difficult to source full cover blocks for. Reference designs are the safest to purchase if you know you're going to waterblock, unless you know in advance that one is made. For a custom board, your only choice is often to choose 'universal' blocks:
http://www.performance-pcs.com/water-blocks-gpu/shopby/vga-series--universal/?limit=90
These can work just fine though, as long as you address the rest of the board with heatsinks and proper air cooling:
http://www.performance-pcs.com/mobo-chipset-mosfet-coolers
to account for the loss of factory unit...