With all the water changes you've done, I don't think Alk or Ca would be the problem. However, zoas will react negatively with low Alkalinity in my tank. Although I've never had swings to the high end, I have had swings to the low end (5 or 6 dkh) a couple times and both times the zoas were some of the first to alert me.
My observations with phosphates is a reduced growth of my zoas and of course increase growth of algae. However, they haven't closed up for days like my issues with alkalinity. Now with that said if algae or cyano irritates them they may close up from time to time.
As Grandis said, I'm one of those that seem to have good results with LEDs and like them. However, if I remember right from my reading, LED intensity drops by something like 2.5 to 5 percent a year depending on heat on the LED. For some of the newer CREE LEDs that's probably not a huge issue, but I would suspect it might be a problem for some of the older LEDs.
Hopefully, changing the substrate will work for you.