Transparent Shapes and States

Hello JeffreyRiley-9e​ 

I'll start by saying, it's hard to fully understand what you're experiencing without seeing the project file, but I'm happy to share some initial thoughts on each of the concerns listed here.

Having problems deciding how to do what it is telling me.
The accessibility checker flags potential issues and directs how to resolve them. Which issues are you having difficulty with? 

How do I set the order when the layers are meant to be pop-up information?
We do have some information on making layers accessible. Are you having a specific issue with the focus order?

The problem is that it has transparent shapes that bring up images on hover.
You're right, hover-only interactions won't work for keyboard or screen reader users. Have you considered turning them into buttons or using triggers instead of hover?

Those images have a lot of text that is too much for Alt Text.
Are you describing images with text? That's generally not a good idea for accessibility. If the information is too much for alt text, you may want to consider a text box that can be accessed by all learners.

How do I help the keyboard or screen reader tell the person what is going on?
Based on your description, create an alternative to hover states, consider text boxes instead of images with text, use clear focus indicators, and provide clear instructions for all learners.

The Accessibility Checker tells me I have to have the video controls on, but I do.
Do you mean that the accessibility checker is flagging this as an issue you think is resolved? It would be great if we could take a look.

It shows me things that I have working, but why are they appearing on the list? 
Resolved issues can still be displayed if not filtered out, and the checker doesn't always know if you've resolved the issue differently, which is why the skip option is available.
When you share your file, let us know which flagged issue you're referring to so we can examine it more closely