acid bath and the after math

[Masonjames]

What condition was the rock in prior to the acid bath?
If there were any orgaincs that were present on the rock the acid will have no real effect on those orgaincs. Even at 100% the acid just isn't going to cut it with organics. This is why bleach is recommended prior to the acid treatment. The bleach is done to prepare the rock for the acid. So what you may be seeing is orgianc material that is still present.
Now if the rock was free of organics, you may just be seeing mineral deposits.

The process is so very simple. And does not need to be made more complicated.
Soak the rock in bleach for 24 hrs. Does not even require diluting. Rinse well when done.
Let rock completely dry.
Treat with acid. Strength of acid will be based on the density of the rock in question. This is up to the user to determine by trail and error. Soak it, bathe it, dump it directly on straight from the bottle. It don't matter. Figure out what works best for the rock in question. Rinse well and it is ready for the tank.
There is no need to neutralize the acid, there is no need for hours of soaking in the acid. Calcium carbonate is an acidic nuetralizer. The rock starts to neutralize the acid as soon as it comes in contact. The reaction happens rather quickly and the acid will be neutralized rather quickly.
Calcium carbonate is used in many industries as a acidic neutralizer. The chemical equation is easily found online.
There is no possiblity of bleach and or acid contaminating the system if the rock is allowed to completely dry after using the bleach, and a good rinse after the acid.
The only real investment in time to do the proccess is soaking the rock in bleach for 24 hrs, and letting the rock completely dry out post bleach. Everything else even the acid treatment should take minutes not hours.