For a 15,000+ gallon pond your filtration is whofully inadequate I'm Afraid your best bet wold be to go to a koi dealership tell them your problem and get some serious filtration for the pond that way you wouldnt be having the problems your having now.
Personally I would have put two bottom drains in when you built it, sadly thats too late now unless you want to drain everything and start again adding the bottom drains then connecting them up to filters man enough to handle 15,000+ gallons.
Did you build it yourselves or did you get a pond builder in ?
We only run a small 1,000 gallon pond but it has the bottom drain and four filters that are overkill, you see our pond is a retro fitted former Koi Dealerships Quarentine pond capable of holding a huge number of koi.
Because my wife and I have disabilities and a lack of space to put in anything bigger 1,000 suites us just fine .
By the way a depth of three and a half inches is also the wrong depth to be keeping koi it is recomended a koi pond be between 4-5ft deep especially if you suffer harsh winters I take it however living in Texas you dont get them ?
You say 15,000+ gallons do you know exactly how much because the odd 15,000 + gallonage should be exact not give or take like you have, this comes in important when you need an exact messurement for treating the pond.
rgrds
Dave