You could do a 2 pump set up, if you want. One pump (1000 gph min) for the full system, and perhaps another 500 gph to discharge right above the water fall to make it more impressive.
Use a hybrid pump. They are the most efficient for gallons moved per watt. That style of pump works better with somewhat larger pipe. For 1000 gph pump perhaps 1-1/2" PVC. 2000 gph, perhaps 2" pipe? When in doubt, over size it, anyway.
And if you need to make 90 degree turns get sweep 90s or use a couple of 45 degree fittings. The extra cost of the fittings is more than made up for with the reduced pressure loss of the gentler turn.
Rigid PVC or flex PVC are the most commonly used tubing/pipe in that size. These are completely fish safe when the PVC cement has cured.
Bio media can go wherever you want, but with plants, pots, soil and so on there are so many lodging sites that unless you are planning to way overstock the pond I would not go crazy about bio media. However, why not add perhaps about 50 gallons of volume at the very top? This would be a chamber for all the media you want, sponge, bio and anything else. Then the water falls into the stream and so on.