Just wanted to take a moment and update this thread in case any finds it in a search down the road or something.
I haven't seen any dinos in the tank for about three months now, and am fairly confident that they are gone. Here is what I did:
1. I came to the conclusion that my sand bed was the issue with my tank. As the tank was only 1 year old, I figured it was worth the risk to remove most of it, and run the tank with a +/- 1" sandbed going forward. Started doing 5 gallon water changes about three times a week, siphoning out sand with each change. Took about a month to remove about 75% of my sand, and take the sandbed from around 3-4" down to an average of about an inch. I was lucky that because the sandbed was young, I didn't disturb any nasty pockets during my siphoning/stirring. Honestly amazed at what this has done for the tank. I pulled my biopellets about six weeks ago, and have not used any GFO in months, and yet my PO4 is testing 0.00 on the Hanna Checker (the low range as well as the Ultra low range). My NO3 has been about 3-4. The amount of filth and gunk I was pulling out of the sandbed was disgusting. I have since added a Diamond Watchman Goby that is doing a great job of stirring the sandbed.
2. When I originally designed my sump I did it in such a way that the dry compartment that held my recirculating biopellet reactor, could be turned into a wet refugium compartment. I went ahead and filled this up, and added a ball of Chaeto to this compartment and a Reefbreeders "fuge light" (high powered RED LED light). Fired this up at about the same time I started removing the sandbed. The Chaeto ball serious went from a tennis ball sized clump to a mass about 10" x 10" and 3" thick in about a week. Growth has since slowed way down now.
3. Added a fan to run over my external overflow, and dialed the chiller down to run the tank between 78.5-79.5 degrees (from 80-81 before).
4. Since I had removed the biopellets and the tank was no longer ULNS (if it ever truly was as the sandbed was definitely chocked full of nutrients), I slowly over the course of about 4 weeks bumped my Alk from 7.5 up to 9 dkh.
5. I did slightly reduce my photo period down to five hours, but didn't do any black-outs, etc. Honestly, the more sand I stirred and removed, the fewer dinos the next day.
6. Finally, I bought a 16 gallon frag tank, and plumbed it into my main tank sump. The frag tank sits right next to the display, and I have a separate pump sitting in the sump, that first feeds the chiller, then into the frag tank, which then drains into the refugium compartment in my main sump. I added about twenty pounds of additional live rock to the frag tank, which I feel bumped up the overall filtration of the system. I plan to add different kinds of macro algae, and a few corals to this tank as a sort of second refugium/second display tank.
Anyway, I don't know if I had the typical nightmare dinos that you read about, but they were definitely a problem, and I fought with them for around 4 months and lost a lot of coral in the meantime. I will never run a tank with more than a 1" sandbed again that is for sure. No doubt many people have good luck with DSBs, so not knocking them, but for me the shallow sand bed with lots of sifters seems to be the way to go.