AES GCM encryption, authentication and PBKDF2
Is it safe to generate IV along with KEY from PBKDF2 when using and storing salt for each user or should IV also be randomly generated and stored along with salt? When generating IV from PBKDF2 I'm basically choosing for it to be part of the key, ie a secret. Using a sufficiently large salt per user would guarantee that no two generated KEY/IV pairs exist even if users have same passwords.
  


Sure thing, but I would recommend to use a KBKDF such as HKDF on the output of PBKDF2 instead of generating a larger output. The reason is that PBKDF2 doesn't handle large output well. That is: output larger than the underlying hash size.


  
  Should randomly generated master KEY pair be stored with both KEY and IV encrypted or should IV be stored in plain text?
  


Inconsequential. The IV can be stored in plaintext as well. I'd recommend this as key wrapping is often thought as a specific routine, and it won't include the IV. Furthermore, you probably need more than one IV (see below).


  
  If you store both encrypted, it is safe to store them in two separate records or should they be encrypted together (concatenated) and stored in a single record? This is regarding IV reuse since two records are now encrypted with same KEY/IV pair.
  


You need to create a fresh IV for each record that you encrypt. If you have trouble storing the IV then you should consider Format Preserving Encryption (FPE).