My guess would be that the coral residue raised your TDS
high enough to affect the respiratory process in the fish. I find it highly unlikely that you got that significant of a change in pH that quickly. Personally, I run many of my African tanks with aragonite sand or CC substrate. Can't say I'm real familiar with the fish you were keeping, but the change in pH should have occurred slowly enough that it wouldn't kill fish. Make them uncomfortable perhaps, but shouldn't have shocked em to that extreme. Personally I think if you give the existing structure a very good rinse job, you should be able to use it as is.