*sigh*, I read your post and though "wait, did I accidentally post under another canreefer's login?".
I've done exactly this. Recently. Expect some SPS to bite it, no matter what you do. Only advice I can offer is that if you've got a piece that's not recovered and sending out new growth tips in 6 weeks, you're almost better off chiselling it out and putting something new in it's place.
Yes, recovery is possible, but after something like that, SPS (acropora in particular) need to be in pristine conditions for months - like 6 months to a year - to make a full recovery. The ones that are most affected (most dramatic colour change, biggest change in PE) will be at imminent risk of RTN every time your alk wavers a few points for the next half year at least.
That said, some species of Acro seem to be able to tolerate those kinds of swings and bounce back relatively quickly. No surprise, those are the ones more common in the hobby. The rarer and more expensive they get, the less likely they'll forgive you for something like that.
It's a funny catch 22 that as your tank establishes and you feel like you've got it dialled in and get complacent, the need for you to pay attention to your tank actually increases. As you colonies grow, the water to coral ratio shifts in a dangerous way. Relatively speaking a mature, jam packed 1000 gallon reef tank can be in the same risk category as a 3 gallon pico in terms of parameter swings. One cracked hose can drop your alk to coral killing emergency levels in a day.
Anyway I feel for you. There's nothing you can do now except stay on top of equipment and parameters and remove anything that's taking more time and effort than a new, prettier coral in it's place would.
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