Ok, a lot to unwrap here. Instead of responding to everyone individually, I'll just try to hit the major points.
Lighting:
Here are my par readings
Most of my frags were on the rack on the left, around 400 par. Some were mounted on the rocks. All of them are getting at least 300 PAR. I'm seeing issues develop across all frags, regardless of lighting. So I suspect lighting is not the issue.
Nitrates and phosphates:
Yes, that phosphate levels were something I was struggling with. I was dosing 5 mLs of neophos a day with no increase in phosphates until I removed my chemipure blue. Then I was able to get it to acceptable ranges. I don't always record when I test for phosphates but I test at least every other day. It's been fluctuating between 0.03-0.1. I still have to dose about 5mLs a week to keep it there.
Even when it was low, I believe some phosphates were present in the system because of how much I was dosing, but I do believe this could have been a potential issue. it's since been corrected.
As for nitrates, I can't get them up above 2-3 ppm. I could turn my skimmer off completely, as they were higher before I started using it, but I know many people have success at these levels and I'm trying not to change too many things at once unless there's clearly something wrong. Maybe I'm in the wrong here, and I'm open to being convinced to shut the skimmer down.
Feeding:
I feed heavily. Probably a little too much. I have 5 fish and I feed once daily. Usually a cube of spirulina mysis or tdo pellets. I could up my feeding to twice a day.
I have been dosing amino acids almost daily, probably about 5 drops, which I think is about a quarter of an mL. I'm considering stopping this and simplifying things. I also feed my acros with reef nutrition oyster feast once or twice a week. Occasionally I use reef roids in combination with this.
Alkalinity:
Ignore the chart. In the table you can see roughly how quickly my alk changed. I test more often than I record. In my opinion it was a gradual increase. I do test in the afternoon each day.
Dosing:
Kalk does keep up with my alkalinity demands. Most my stony corals are small frags right now and I use a fully saturated kalk solution, not a slurry. I do this over 2 part because it's cheaper and I want to keep my pH higher. I don't really have interest in changing this. Many people have success with kalk and I don't see this as the issue.
Leathers:
I'm considering removing some of my leathers today. It's a shame because I don't have anywhere to go with them, but I don't want to let a $20 leather kill $300 of acropora. This seems like a safe adjustment to me. The problems did start around the time the devil's hand leather started getting stung, so maybe that is part of the problem. Also, with no activated carbon after I removed the chemipure, maybe there's some toxins in the system that were being removed before.
Overall thoughts:
I'm leaning towards the leather causing problems. I had phosphate issues, but I've since improved my levels. I may look into raisin my nitrate levels. I'm weary of changing a million things at once because corals are already struggling. Thank you all for your suggestions. I'm certainly not giving up here. I'm actually in the process of setting up a 120g tank! I love the challenges reefing brings even if it's sometimes frustrating.
Lighting:
Here are my par readings

Most of my frags were on the rack on the left, around 400 par. Some were mounted on the rocks. All of them are getting at least 300 PAR. I'm seeing issues develop across all frags, regardless of lighting. So I suspect lighting is not the issue.
Nitrates and phosphates:
Yes, that phosphate levels were something I was struggling with. I was dosing 5 mLs of neophos a day with no increase in phosphates until I removed my chemipure blue. Then I was able to get it to acceptable ranges. I don't always record when I test for phosphates but I test at least every other day. It's been fluctuating between 0.03-0.1. I still have to dose about 5mLs a week to keep it there.
Even when it was low, I believe some phosphates were present in the system because of how much I was dosing, but I do believe this could have been a potential issue. it's since been corrected.
As for nitrates, I can't get them up above 2-3 ppm. I could turn my skimmer off completely, as they were higher before I started using it, but I know many people have success at these levels and I'm trying not to change too many things at once unless there's clearly something wrong. Maybe I'm in the wrong here, and I'm open to being convinced to shut the skimmer down.
Feeding:
I feed heavily. Probably a little too much. I have 5 fish and I feed once daily. Usually a cube of spirulina mysis or tdo pellets. I could up my feeding to twice a day.
I have been dosing amino acids almost daily, probably about 5 drops, which I think is about a quarter of an mL. I'm considering stopping this and simplifying things. I also feed my acros with reef nutrition oyster feast once or twice a week. Occasionally I use reef roids in combination with this.
Alkalinity:

Ignore the chart. In the table you can see roughly how quickly my alk changed. I test more often than I record. In my opinion it was a gradual increase. I do test in the afternoon each day.
Dosing:
Kalk does keep up with my alkalinity demands. Most my stony corals are small frags right now and I use a fully saturated kalk solution, not a slurry. I do this over 2 part because it's cheaper and I want to keep my pH higher. I don't really have interest in changing this. Many people have success with kalk and I don't see this as the issue.
Leathers:
I'm considering removing some of my leathers today. It's a shame because I don't have anywhere to go with them, but I don't want to let a $20 leather kill $300 of acropora. This seems like a safe adjustment to me. The problems did start around the time the devil's hand leather started getting stung, so maybe that is part of the problem. Also, with no activated carbon after I removed the chemipure, maybe there's some toxins in the system that were being removed before.
Overall thoughts:
I'm leaning towards the leather causing problems. I had phosphate issues, but I've since improved my levels. I may look into raisin my nitrate levels. I'm weary of changing a million things at once because corals are already struggling. Thank you all for your suggestions. I'm certainly not giving up here. I'm actually in the process of setting up a 120g tank! I love the challenges reefing brings even if it's sometimes frustrating.