It is not HD wallet. Addresses started with "1". Keys encrypted independently or in some big chunk?
AFAIK it should be in one big chunk (located on similar byte location), but each private keys should be encrypted independently.
This PBKDF2 key stored in some fixed place? It is possible to find them manually?
Unfortunately, i only know high-level information about Bitcoin core wallet & i don't know if PBKDF2 was used on older version of Bitcoin Core wallet.
But there are 2 core developer who's active in this forum, your question should be answered few days later.