(The maintenance manual for one Varian leak detector actually said to clean the blades of a turbo by partial immersing in Freon TF. Not gonna happen now.)
This is where a manual is essential or call the company.
I haven't had any luck getting maintenance manuals but I did have some luck talking to someone who works at Ideal Vacuum Products.
The user manual for this pump has a cutaway drawing. Assuming it's accurate, I should be able to soak the pump to a depth that will get the drag stages but not the bearings. However, the bearings don't look like they are protected by a "shaft tunnel" unless you know for sure.
In any case, I think I have an idea of a path forward.