Thanks for the responses.
Build Thread: I do have a build thread although I need to update it more frequently.
Copper: I only checked for copper because I do have a QT going in a separate room (far away) with copper and figured there was a minute chance of cross contamination, but based on the Hannah checker I don't think that's my issue. Any cross contamination would have been miniscule and the polyfilter I'm running would also remove copper so my gut tells me that's a dead end.
O2 Levels: I have not manually checked O2 levels as I don't have a test kit for that and from doing a little reading it doesn't seem to be something most people test. However, based on my prior issue I may order the Hannah kit for it. I did turn down my HOB filter recently to a lower setting and I think I'm just going to leave it at full blast from now on to maximize surface agitation. I run a glass lid and I know there's some debate on whether those have a meaningful impact on gas exchange.
Salinity: I don't have a second way of testing salinity but I reconfirmed the calibration today with calibration solution.
Water Changes: Last change was a 40% water change a week ago. I try to do about 30-40% every week or two.
New/Cheap Shrimp: I have considered buying a peppermint shrimp next as they're considerably cheaper. It's not quiet as entertaining as the skunk but wouldn't be a bad tank addition.
My Thoughts: Based on my recent issues with O2 I lean towards this being the most likely issue if there is indeed something wrong with the tank. The shrimp was not very active when purchased so it's possible he would not have made it BUT my trochus snail not moving for over 24 hours (except for small wiggles) during this same time period makes me suspect something is off. I have 3 total snails:
Cerith: oldest member of tank. Survived all issues but seemed inactive during the worst periods of the bloom. Hard to know for sure since he sleeps in the sand during the day. However, I've seen him much more since the bloom and water has cleared. Was very active last night.
Trochus: bought on trip before discovering tank issue that I had a several weeks ago. Was fairly inactive when first added (a week or more of very little movement). However started moving normally and was roaming all over the tank including the glass for about 2 weeks until this recent 24-48 hour inactivity period.
Nassarius: bought this 2 days ago before the shrimp died or noticed trochus not moving. Bought specifically to help with aerating the substrate which I felt was a contributing factor to the bacterial bloom. Too early to make a call on his activity levels, but was surprised it hasn't come out during tank feedings. Some movement seen though.
I know cleaners are extremely delicate and some people don't even recommend them in smaller tanks while multiple reputable sources say it's totally fine. I tried to research if inverts or fish are more sensitive to O2 changes, but could not find an answer. Some things said larger organisms should be impacted faster, but I also read it's highly variable by species. I did find this quote from sciencing.com "Aquatic invertebrates are highly sensitive to minute changes in dissolved oxygen, and in general, higher dissolved oxygen leads to more life and more invertebrate activity." I also found a scientific paper where they studied different fish/inverts and recorded different sensitively levels but it doesn't cover any species I own so I can only extrapolate generalizations.
The original surviving clown seems totally fine. No odd behavior to suggest he's struggling for oxygen, but he also survived the initial bacterial bloom that killed the first clown and was showing no signs then. He got hit about 11 days later when the bloom resurged post water change.
Here's my plan at the moment:
Do things that will obviously raise O2 Levels: I figure none of this can hurt but it could help. I've turned the HOB up to max for more surface agitation. I've also done some manual agitation with a cup and opened up the lid. Plan to leave it open a good deal of the day. I would drop in an airstone, but I'm using my other pump to run a qt right now for the replacement clown mate. Probably going to go ahead and order a 2nd pump/airstone and drop it in once it arrives. A little extra security wouldn't hurt.
Turned UV Up to Max just in case the bacteria is starting to rebuild. I set it to the minimum flow level after it totally cleared my bloom and did a large water change because I can't run it at higher settings and my wavemaker at the same time or it's just too much for the fish and he can't move freely. This being the case I've turned UV to max and turned off the wavemaker for now. I also moved the UV outlet closer to the surface to further help with surface agitation.
I'm hoping that the trochus will start moving again within 24 hours or so. If it does then I might try my luck with a peppermint shrimp. Some seem to suggest they're hardier than cleaners. They certainly come from less far away so I figure that's a factor and they're considerably cheaper. Alternatively, I'll just wait a few months until I upgrade tank sizes and get a new skunk then. It might come down to how many questions my kids ask in the mean time. I know they're highly sensitive creatures so regardless of what lead to it's demise, a bigger tank should be beneficial.
On the plus side all my coral looks great. The GSP is fully extended and even extends a large amount during the night. The Xenia seems to have at least doubled in size in the 3 weeks I've had it. Both looked fairly poor when first adding before the bacteria issue was discovered and fixed, but have looked fantastic ever since the water cleared. I also have a new frogspawn frag I bought at the same time as the nassarius. It came right out after introduction and looks good.