How low does your PH drop at night. Your tank is well stocked so there must be significant coral respiration at night that would add a lot of Co2. A reverse photoperiod refugium would keep your nightly dissolved oxygen rates high and balance PH if that in fact is an issue.
I have mixed feelings about cutting back flow at night. On one hand it replicates natural reef conditions and allows plankton to get around better at night, but on the other hand it may lower dissolved oxygen, make it harder to off-gas Co2, and higher flow may be better for feeding extended night feeders.
Whatever you are doing right to keep phosphate and nitrate at zero appears to be great for your SPS, and not so good for LPS. I would guess that it's the low nutrients and not high toxic metal concentrations that are limiting LPS success.
Rather than limit what you are doing right (nutrient reduction & export through protein skimming and water changes), I would increase nutrient import with Phytoplankton, rotifers and whatever you prefer to feed. I've read a few threads on RC about dosing phosphate and nitrate, but I think they should be added via food, not chemically.
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