Hi @opaquebrace,
Sorry to hear about the unnecessary stress. That is certainly not the intended goal of any part of the process. It should be somewhat self paced, I am surprised that there is any part that would time out like that, unless you were doing over a long period of time (like more than 24 hrs). The one time passwords expire, but you would be immediately issued a new one, there is no expiration on the session, just a new code.
I am not sure what the passphrase part of the application is. It might be a custom option that was created by the brokerage, it is hard to say without seeing it.
A lot of this process is controlled by tradestation. It may be best to give them a call and confirm that everything is working, so you aren’t locked out when the deadline hits. If you have issues I am happy to jump on a call too.