Hi Dean,
I'm planning on installing the same system on a much smaller pond (0.2ac). I'm concerned with this clogging like yours did. Do you know what is on the end of your inlet pipe? Is it just open to the water or does it have some type of trash rack on it? What size pipe are you using (4", 6", other)?
I used a 100' corrugated pipe to drain/siphon my pond recently. It worked really well. Drained in one day. It was easy to start while the pond was high, but restarting when the pond was lower was very difficult.
