I would like to mod my 1080 FE with an ACX 3.0 cooler. Does EVGA sell these coolers separately?  

So the only way to get one would be sites like ebay right?

You probably already know that you can buy aftermarket coolers such as an Artic Accelero Twin Turbo II for around $40 at Newegg other places and comes with VR and VRAM heatsinks..And sometimes also a junk card for parts on eBay like bcavnaugh said.

If you're just looking to get the GPU temp down, you should try Thermal Grizzly Conductonaut liquid metal TIM for about $15 at Newegg other places..The stuff is awesome with a whopping 73 W/mk of Thermal Conductivity..You can see my amazing before/after GPU results here in Post #12..I'll never use anything else again.

If you're going to try Conductonaut, you should apply a couple coats of clear fingernail polish around the GPU chip to protect the things in the surrounding area from any conductive metal that might get squeezed out upon reassmbly, but it only takes an extremely small amount to cover the GPU chip and heatsink.
 
I suppose the ultimate thing to do is put a better cooler on it along with Conductonaut.