I would get the CO2 levels back to normal first (having them steady is the most important part).
Why do you have two airstones running if you are injecting CO2? If you have them running when the CO2 is being injected, you are probably losing the CO2 faster than it can be dissolved into the water column, effectively making CO2 injecting moot.
As you mentioned, your EI dosing could be a little tighter, but with your nutrient levels as they are, it might be OK.
I would keep everything as it is now (but get the CO2 levels steady), and use some glutaraldehyde (Excel, Metricide, API CO2 booster, etc) or hydrogen peroxide and spot treat the BBA affected plants and/or hardscape (hardscape can also be removed and given a bleach bath).