Programming EPCS via NiosII IDE

Your steps look just right to me. Except you shouldn't have to replace the ASMI controller with the newer EPCS controller.

It is true that we generally recommend the EPCS controller over the ASMI component. However the flash programmer design contains an ASMI for a reason. The main difference between the two components is that the EPCS controller contains a bit of on-chip memory that allows you to boot a NiosII from the EPCS device (you can't boot from an ASMI). Since the flash programmer design boots from on-chip rom, not the EPCS, there is really no need for the EPCS controller over the ASMI. The reason the ASMI controller was chosen for the flash programmer design is that it does not consume the memory resources the EPCS controller does, allowing the flash programmer design to fit in the smallest Cyclone device, a 1C3. This is why your controller swap is likely the reason you needed to reduce the size of your payload buffer memory.

I suspect your list of steps would also work without replacing the ASMI with an EPCS Controller.