They will send a deficiency letter with your incomplete application with a 1 yr deadline to complete it-but you will not receive an ATT. Everything must be in perfect order, with nothing missing.
I would send everything together (usually you are waiting for the degree to post, and then obtaining an official transcript to include). Also, for the CA intern affidavit, the board will send a deficiency letter if you put hours on BOTH lines.
Our school told me that only 2 CABoP employees process the applications...anything amiss and it's an auto reject. This also explains why it took 6 weeks for them to communicate with me after sending a completed application. This year they are picking on peoples' hours, so be warned.
Seems like Western U was much better organized than USC (and submitted applications much earlier). Both those schools sent out applications batched as a class. And the board processes everything first-come, first-serve.
The next NAPLEX opening in 2 adjacent counties is August. I am hearing that people are going to Vegas, Fresno, etc (4+ hrs away) to take the exam in a timely manner. Not sure if this helps, but I wish you much luck!