You can overcome this... my tank just went through most of the same (minus the nudibranchs).
Sorry to hear about the fish loss. I love my pistol/fish pair, and lost my first paired up fish during the early months of the tank. Thankfully, the pistols are resilient, and pair up quickly with new fish.
I don't have any experience with nudibranch pests, hopefully someone else can help.
As for the flatworms, that I have very recent experience with. I did pretty much followed the approach you are proposing. I siphoned, dosed with flatworm exit, water changed, and repeated a month or so later. From what I have read, it is hard to overdose that stuff in the tank. I will say some of those little buggers seemed immune to the treatment. So I added a Six Line wrasse. He seemed to help the most.
Best of luck!