In my experience with KNC's 28nm hardware,  the primary thing stopping overclocking/better performance, was heat management.  The best solution was to make sure the underside of the board is cooled as well... even just placing a high speed fan on the bottom of the boards worked wonders.  I suspect that the neptune will be harder to overclock (the female pci-e connector and VRM's seem pushed hard on normal clock speeds, for one),  but having some sort of mounting solution to better cool the top and bottom of the board might be a good place to start. You could do this by having the metal sheet that you mount it raised slightly, and place vents underneath the boards (or cut little asic sized holes) to give room for some high powered fans on the bottom.  An even better idea might be to mount the boards upside down,  and give a place to mount fans on the top of the sheet, with holes in the sheet to allow air to go through.

If one were watercooling these boards,  I suspect that mounting them on their side might work really well also.  That way you could put, say,  a nepton 280L on the top side of the board,  and have a high powered air cooling solution on the other side/both sides to keep the VRM's and that PCI-e port cool.

Just some thoughts...