I'd be selling those extra koi to offset any cost of renovating the pond. Have you looked into physical filters/media?
I'm no expert but Bill seems spot on here...any time I've seen a nice population of koi in a pond (there are a few big ones around this area) the water quality is always terrible.
You might want to check these folks out. Kloublec's sell koi, filters, supplies, etc.
https://www.kloubeckoi.com/
