Bottom drain/wet well and or skimmer?
Skimmer on opposite end of falls will create good flow. It might require a slightly larger pump since it will have added head pressure from the long run of pipe, and the height needed on the falls.
Orginal size pond plus a little added depth and a 12' stream should be perfect.
Smaller gravel on the bottom would be better. Larger river rocks/bouldrers, even only 2-4" round will create many small pockets for detritus to collect. I would use a smaller, smooth, washed gravel such as pea gravel or similar. This way debris will settle in top of the substrate and be able to be removed mechanially easier if fish or airstones keep it suspended. Do not exceed 3" in depth of the gravel.