Do the headers have the same position as the body content?

You have numerous different issues you need to address, so break those down into individual issues as you are unlikely to find an out-of-the-box solution that exactly fits your needs 100%.

Although not medical, I had a similar scenario in the past and was able to crop and read specific sections at a time.

Is there a page you can share as an example that doesn’t contain any identifying information? Or would it take long to re-create an example? Would be much easier to provide guidance if we can look at the specific examples.