AES file encryption with PBKDF2. Safe parameters?
As this question is still on the list of "questions without answers", I'll quickly answer it (Basically repeating all of the above comments).


Increase iteration count to something larger (1 Million?)
You don't want to attach your HMAC of the plain-text after the contents. Rather authenticate either the ciphertext or (even better) use CCM/EAX/GCM mode.
Store the PBKDF's params in the header of the file.
Don't use PBKDF2 if possible. Rather use scrypt (best choice currently, for the next weeks), bcrypt (if no other option) or some of the PHC finalists.