While TCP port 22 is the general right answer, this is dependent on the fact that SSH is configured to use the standard port and not an alternative port.

As SFTP runs as a subsystem of SSH it runs on whatever port the SSH daemon is listening on and that is administrator configurable.

Since the data is clearly both important and sensitive from your clients' perspectives, I'd suggest you consult a security professional. Home-grown solutions are typically a combination of over- and underkill, resulting in mechanisms that are both inefficient and insecure. Consider:

• The files are pre-encrypted, so the only gain from SFTP/HTTPS is encryption of the session itself (e.g. login), but...

• You're using PKI for upload and OTP for download, so there's no risk of exposing passwords, only user IDs -- is that significant to you?

• How will you transmit the one-time passwords? Is the transmission secure?

• Keep in mind that any lockout scheme should be temporary, otherwise a hacker can disable the entire system by locking each account.

Questions to ask yourself:

• What am I protecting?
• From whom am I protecting it?
• What are the attack vectors?
• What are the likelihoods and risks of a breach?

Once you've answered those questions, you'll have a better idea of the implementation.

In general:

• Your choice of AES256 + salt is very reasonable.
• Multi-factor authentication is probably better than multiple iterations of encryption. It's often thought of as "something you have, plus something you know," such as a certificate and a password, requiring both for access.

As far as available utilities, many off-the-shelf packages are both secure and easy to use. Look into OpenSSH, OpenVPN, and vsftp for starters.

Good luck - please let us know what method you choose!