Can a CPA working in a bookkeeping firm prepare the Annual Financial Statement (AFS) report?

No.  The AFS report must be conducted by a CPA operating within a CPA firm. The AFS report is an agreed-upon procedures engagement which is an attest service. In accordance with the American Institute of Certified Public Accountants (AICPA), only CPA’s operating within a CPA firm can provide attest services. View the AICPA CPA Services chart here for more information.