I appologize if this is redundant (I
did read everything) - my suggestion is to soak the entire filter setup in methylene blue next time you do a major cleaning. You'll kill off any invertebrates it touches while maintaining the beneficial bacteria colonies (I'm pretty sure it doesn't kill bacteria. Not 100% though). I had a turtle tank a few years ago that got mobbed by snails, and I kept M-Blue in the tank for about 3 weeks and they never came back. Didn't have to strip it down & bleach or anything like that, just kept dosing the water as if I was treating ich and it worked like a charm.
Also -
very nice setup!! I'd LOVE to have a bunch of natives with my snapping turtle but it's a just bloodbath waiting to happen
Looking forward to more pics, I'm def subscribing to this thread!
Hope this helps & best of luck to you sir!