You reactivate your license for a 6 month period. You can then upgrade to whatever version of the software is available at that time. 4.0.7 is currently available and would cost you the $45 that you listed, per site. You can download any new version that is released within your 6 month window.
3rd party. There are 2 specifically that my members would have major problems without. There have been a lot of new 3rd party apps developed, but the updates from 3.X to 4 have been a little slow. I'm hoping that the release of 4 will help to get the updates rolling.