Whatever caused your stn, it seems like it is slowing or going away. You've adjusted so many things and if you think about it, you've "eased up" on your system. Take for example the temp, at the low end, alk was getting low, lighting possibly on the high end (although I don't remember a par measurement so I'm not sure) and if you got "something" in the tank to start the domino effect then this could all make sense and hopefully you're on the upside. Stability and water changes should get you across the finish line.
With your lights being on the tank so long and unless your pumping 700-800 par out, I don't see that being THE reason..... Same with temp, alk etc etc.
You've seen my sps tank, led with recent t5 retros that has been up and running for 2.5 years. Temp goes from 78-80 depending on the time of year, lighting is putting out 500par mid tank and the alk has been in the 7-8.5 range over that span.
You may never know the reason and I wouldn't switch anything out (don't think anyone is recommending that) so keep it stable and change out the water and you'll be set.
Swing down my place one day, I'll give you a few sps to replace what you lost