@Humblefish , very sorry about your bad luck with this round of treatment. I echo the comments above, you've saved more fish than you know through your advice.
I'm going to provide a summary of my ongoing treatment, as it was very similar to yours. Hopefully this will help. I'm going to provide as much detail as possible, sorry if it's a long post!
Setting the stage: I had 6 fish in my tank, most of which had been with me for years. In the past I haven't properly QT'd, but the worst I ever saw was an occasion spot or two on my extremely skittish Foxface. About 2.5 months ago I purchased a juvenile kole tang. I was about two weeks into passively QT'ing him (no meds) and he looked super healthy and was eating well. Then a work trip came up, I had to leave in two weeks. I had to make a decision to either teach my lady how to feed, observe, monitor ammonia, mix/change water, etc.. or put a healthy looking fish into the DT. It was a tough decision. I decided to put the kole in immediately, giving me two weeks to observe before leaving. He looked fine the entire time, until the morning I left. He was covered in white spots and swimming rapidly:-( Had to leave for the airport..
Speeding things up: When I got home the kole tang had vanished. Adding to the chaos, my apex auto feeder didn't feed while I was gone. The fish looked horrible. I started feeding heavily, hoping they would turn around. My two anthias had ragged fins. Within a few days one was lying on the sand breathing rapidly. That was the last I saw of him. Started planning for treatment. Then my ORA orchid dotty back showed ragged fins and a huge gut. Found him dead the next day. My fox face had huge black spots on his side, this clearly looked like black ich. I also noticed what looked like powdered sugar down his back at certain angles. I assumed this was velvet. As I was pulling my two clowns out, I noticed sloughing skin/mucas on their foreheads. Brook? The first day in QT I noticed white stringy poop from one of the clowns. Internal parasite? It seemed like they had everything! I decided to start treatment for velvet as it seemed the most serious, and black ick as I was the most certain about it. Here's how the treatment went.
Day 1: CP* dose and prazipro as per instructions. Fox face breathing very heavily (w/ proper aeration), skiddish, not eating. *Important to mention that I used NLS Ick Shield. Couldn't get pure CP quickly, but all reviews I could find said Ick Shield worked well.
Day 2: No dose. The black spots were gone as was the "powdered sugar" on the back of the FF, leaving raw patches in the areas where the large black spots were. Fish still looked "sickly", though. Clowns and anthias eating, FF would not.
Day 3: No dose
Day 4: Fish still look sickly. Ruby reef rally arrived, did a bath.
Day 5: All fish looked remarkably better. From this point on, no spots, sloughing skin, or any external marks. FF still breathing heavily, skittish, and occasionally swimming erratically.
Day 6: Kanaplex and metroplex arrived. Dosed both. Kana to prevent secondary infection, metro b/c of white stringy poop noticed on first day.
Day 7: Very cloudy water, no other changes.
Day 8: Clowns and anthias eating, but barely. Make a decision to skip kana and metro.
Day 9: Anthias stops eating.
Day 10: Foxface still not eating. Anthias suddenly found dead. Started to rethink treatment.
Day 11: Resumed ruby reef rally bath as all fish seemed to look much better after the first bath. Also started metro as I was starting to suspect internal parasites as the cause of the anthias death.
Day 12: Looking better. FF still hasn't eaten.
Day 13: Dosed metro.
Day 14: 12 hour bath in bucket with ruby reef rally as I sterilized the QT and all equipment with vinegar and let dry in the sun. As I was removing the FF from the bucket with a colander, he jumped out onto the floor. I put the colander next to him and he flopped halfway back in. I reactively reached down, and yeah.. ouch! Felt like a bee sting for about 5 mins. Haven't noticed any damage to the fish yet.
Day 15: Back in the QT, no meds. ALL FISH EATING VORACIOUSLY!
My plan going forward is to just feed and observe. One thing that I'm pretty excited about is the ability to use ampule now. The 50% water changes every other day were a huge chore.
The big questions I have:
1. **What diseases did I actually have?** Based on the reactions to treatment, I think it was brook and not velvet. More confident on the black ick and internal parasites.
2. **Did I eliminate them?** (i.e. should I continue metro for internal worms? Should I continue ruby dips? Going to wait and observe for now)
2. What killed the anthias? Disease or meds?
3. Did NLS Ick Shield work? I think so...
Sorry this is so long, but hopefully it provides one more data point regarding treatment.
I should have skipped the FW dip, placed them in another non-medicated QT, and then checked for flukes after they had been eating for a week solid. But I am going to New Orleans this week, so I was trying to get everything setup for my wife to care for them while I was away.
What makes this even worse is I had the bucket resting on a step stool so he had farther to fall. 
