The big picture is that 1) if there is a preference in the product to do what you want, then 2) you can set that preference and it will apply to all PDFs, then 3) you can distribute that setting across machines.
So your solution (assuming the preferences exist) is:
- Get regshot
- Close all apps except Acrobat.
- Go to the preferences panel you need.
- Take a regshot.
- Set the Acrobat prefs.
- Close Acrobat.
- Take another regshot.
- Compare the to registry snapshots.
You now have a list of what's changed.
hth,
Ben