Sorry for my delayed response. We were doing some pre-Halloween activities last night.
Mini-update:
I sent an e-mail to the principal this morning. It looks like we will meet tomorrow or Thursday. I asked to meet with her alone initially -- without the teacher. I have spent the better part of this morning editing my notes from the timeline in my OP so I can share them with the principal and also trying to do some of my own work.

After school yesterday, DS told me that he submitted his research paper for his experiment. He still hadn't turned in the other work that he completed at home a week ago because the teacher told him it should be uploaded to the class website. He didn't know how to do that. He asked her yesterday for instructions on how to upload, and she told him it could be turned in "either way." He surmised that she meant it could be submitted by hard copy or an upload to the website. She didn't give him instructions on how to upload it. After school, I helped him get it uploaded because we don't have a printer at home. I asked DS what was happening the room when he asked for upload instructions. He said there were a bunch of kids there who were missing work and trying to talk to her.
The homework website was finally updated yesterday with a statement that the work for this unit will be due "no earlier than 10/31." DS still says the last day of class time for the unit will be 10/31.
As of a little while ago, a chunk of missing grades had been entered for B- and C-layer work in the online gradebook. It appears that the teacher is working furiously to enter the grades. I will be watching like a hawk to be sure everything is entered.
In the meantime, the only assignment DS has remaining is a quiz over the A layer. He should be able to take that today or tomorrow.
I will continue to post updates as I have them.