Unfortunately old birth/marriage/FBI certificates are not considered valid for your application.
You will need newly issues ones: for birth certificates within last 12 months, for marriage certificates within last 6 months, and for FBI checks within last 3 months prior to submitting your application. And yes AIMA generally requires a new full set of valid documents for biometrics.
The issue date on the certificate is the one that matters. And yes you will need everything apostilled.
Re submitting late, there was some wiggle room during Covid when govt departments in the US were taking longer than usual to issue and certify docs, so Portugal sometimes let you submit the docs well after your appointment. I did read a user on here who mentioned they recently had 20 days from their appointment to submit some missing docs, so it looks like that is still the case, but again, everything needs to be valid.
Welcome to the exciting world of document timing. This is a regular part of the process for application and every renewal.