As someone who just got helped get OpenEMR (another OSS EHR) certified via ONC, I don't envy your journey through certification and wish you the very best of luck.
Looking through your documentation what version of FHIR are you targeting? Are you using SMART on FHIR v2? or v1?
What version of USCDI are you using for your data model? Have you decided whether you'll hit US Core 3.1 or are you going to go through the SVAP purpose for ONC?
One of the biggest questions we get all the time from people is lab integration, and e-prescribe. Is this something you are punting to your customers or do you plan on supporting that out of the box?