AES-CTR-256 Sub Keys With Encrypted Sub Key Index
I would advise a different solution.

You either generate a master-key (or key set) or derive one from a user password (e.g. via PBKDF2 or SCrypt). For each file to encrypt you generate a random key (file key) and nonce ad-hoc, and encrypt the file with that key, using an AEAD scheme.

The random file key is encrypted with you master key and put at the beginning of the file. Preferable you should include that encrypted key as authenticated data within the AEAD scheme.

The steps:


Generate random file key and nonce
Encrypt file key with master key (using a key-wrap spec.)
Encrypt the plaintext file data with the file key and using it enc. form as part of the authenticated data (AEAD scheme)
Store nonce, enc. file key and encrypted data as the enc. file


Your solution is dangerous. Using the same nonce with the same key (you only have 9 or so) to encrypt different data will allow an attacker to retrieve information concerning the plaintext data.