Once approved for FAP, can I submit an ADEA AADSAS application with missing scores, recommendations, etc. to use the waiver within 14 days?

You should aim to submit a complete application whenever possible. However, if you are approved for FAP, you will only need to submit your ADEA AADSAS application within the 14 days given.  If you still have documents to submit to ADEA AADSAS, such as transcripts, you will need to submit these documents to be considered  to have a complete ADEA AADSAS application.