I just rooted a couple of days ago, and had the same issue with the launcher that you have. Do you have the NookLauncher (Home Icon) installed as well as the MyNook ru.Launcher. The ru.launcher comes with the softroot I believe.
I like the NookLauncher better, because you can clean up the home screen with sub-folders and customize the way you want it to look. If you choose that one, after you install it, you want to delete the ru.launcher via adb. Nooklauncher also has a button that sets it as the default.
Sorry, that doesn't really answer your question. Once you choose a launcher it is supposed to default to that in the Home Menu, but I had some trouble with that before I installed NookLauncher. It is irritating.
As for the pdfs loading there is a fix for that here:
http://nookdevs.com/APDFViewer
Not sure about the other questions, but I hope someone comes along soon to help.