I have lots of books from many different sources on my Kindle. I usually have my wifi on at least once a day for downloading an Amazon freebie or email and never had a problem with Amazon messing with my stuff.
I use Calibre to organize my collection and to remove DRM. I agree it's a great program and not sure how I ever lived without it. It enables sharing among myself and my grown daughters who have different ereaders.
The new firmware is no problem. People who wanted page numbers are upset because, although they now exist for some books, you have to click on the menu to see them. They really should have just added them to the actual pages. It makes no difference to me since page numbers are meaningless on an ereader. I find the percentage much more useful.
Another thing people don't like about the new update is that as you finish each book, you are given the opportunity to post to social network sites, review the book, or look at other books by that author. It sounded much worse than it is. You don't actually have to do anything. In fact, you don't even have to go past the last page of the book to get to these options.
I put 3.1 on my Kindle the day it was released and have had no problems with it. I have even used it to make a couple of facebook posts when I've finished books. It's kind of cool, nothing like the pushy commercial people thought it was going to be.