Focus Order, Accessibility, and Set Focus

Okay, I need some help please.

I was contracted by a company working on this gigantic project (over 150 storyline files) that are non accessible and they wanted screen reader accessibility.

Granted, this project has been in the works for 8 years, and changing how they built stuff is not an option. They use a lot of modal layers instead of dialog ones, which seems to cause a lot of problems for Screen Readers.

Every time you open a new layer, NVDA loses focus.

To rectify this, I've added a "Set Focus" on "Text" when the timeline starts on "Text" in the new layer.

This fixes the screen reader, but for non screen reader users, it adds that ugly yellow square that looks like a glitch if you don't know where it's from.

I see a lot of posts here saying Set Focus isn't the best trigger....but when I don't use it, opening layers is a nightmare and I have to find "Back to top" and start over, which can be infuriating, and I would be infuriated if I needed to keyboard nav this project.

I just found out that unchecking "Prevent users from clicking on other layers" seems to make this work without a set focus....but I was keeping that checked because if you use back to top in a layer, you have to recycle from the beginning....and some slides have like....12 layers ... ouff.

Does anyone know what could be done without drastically renovating way too many files and layers?