I vote for the silicone or something chemical in nature. I've had SPS issues myself over the last few months (or really lets face it the last few years, granted they were never any single thing). Anyway, this last one was definitely chemical in nature and resulted in STN of many frags and colonies. I'm at the point now where I think I've diluted it enough and things are turning around. However if you suspect the silicone, it will be leaching out whatever toxic chemical for quite some time before it is exhausted. I think at this point you need to realize that either you can't keep SPS in that tank or that you need to get everything out of that tank and into a different one to save yourself the headache and heartache.
Perhaps you could resilicone the tank with the proper silicone? (ie. get some more from Bow Valley)
Don't know what to suggest about the rock. I would imagine at some point it would stop leaching whatever its been sucking up (if it has been sucking up anything for that matter) however I wouldn't want to take the risk.
Oh and personally I think its good to be nervous of ozone. Less chance of buggering it up. However its not as scary as you think, you don't need all that much to get the job done, IMO, and the amount doesn't harm a thing (well nothing you don't want it to anyways
). I aimed for an ORP of about 425 (although I've heard 360 is "better") using 25mg/L. Clean the probe in vinegar/water
every week or it will throw your readings off.