Grant,
We put in a retro system on a pond that is somewhat simular to what you are doing. 800 gallon settlement chamber that catches 80-90% of even the fine solids.
Then off to the pumps, through a very large bead filter, then through 3 100 gallon upflow in tandem mostly for the biological filtration. They used to have a really fine filter media on them, but we went with 3 different matalla matting, 30 sheets in all. Pond went from 6 inches of visibility and very green water to you can see the fishes shadow at 4 feet. Where he had been only useing the upflow with the old style matting, he had been haveing to spend 5 hours each weekend cleaning the system, now, outside of flushing the settlement chamber and backwashing the filter, he has yet to find any need to clean the upflows, and they are into the 3rd year.
Pond maintenance now takes 10 minutes a week at worst and the results are nice, where it used to take at least 6 hours and did not work.
As far as water quality, you could not ask for more. Each flush of the system each week takes about 400-1000 gallons.
I am of the mindset that no, you can not build it too deep. Unless you are talking greater than 15.
d