f your compounds are (or will be) labelled as USP grade, they should be assayed by the USP procedure or equivalent.
When you validate your new method, you have to demonstrate accuracy. In general, this can be done by comparing results with a reference technique (in this case, your microbiological assay). Since your old assay is imprecise, it shouldn't be too hard to demonstrate that the new one gives values within the 95% (or whatever) confidence interval of the old method.
To be cGMP compliant, you have to follow your SOPs. Hopefully, there is an SOP in place that specifies what you have to do to demonstrate equivalence. If no SOP, write one.