B-ski I've already said this but I'll repeat my self again. You need a trash rack on your intake. Yes it can clog as your contractor stated but it can be easily cleaned. If something of size gets sucked down the pipe and it jams some 100 ft under your dam well call the track hoe out and start digging. Your emergency spillway will carry the water as you've stated if the trash rack every clogs. If the trash rack is designed so that it can draw water underneath it then the pipe will flow even if the rack gets clogged with debris. Just my 2 cents. It's your plumbing do as your wish.
By the way how many sq ft you want it and will it be 1,1.5, 2, or 3 stories? 4?
