Hi
@greenesthash and welcome to the forum!
Once the fermentation has occurred, the vinegar and the eggshells are converted into calcium phosphate. It will no longer kill your plants. And yes, the pH of vinegar starting out is quite low, and even after the fermentation the remaining compound remains so, but there is no adjusting necessary. At the rate you would apply this, typically 1 tablespoon per gallon, it is not going to affect the pH of the final mix very much at all. You are overthinking this.