MacOS – ny stable Adobe Reader for OSX

Probably this is not possible with Preview, but there is another (free) PDF reader that allows you to do this (at least your first three points, don't know about converting into another annotation kind): Skim.

After you've opened your PDF in Skim, you can choose Convert Notes... in the File menu. Then you have all your notes from Goodreader in the drawer panel on the right.

The problem seems to be that automatic wakeups from the sleep state fail, possibly because of driver-related problems*. My workaround is to simply disable automatic wakeups — and even automatic sleep. Since for me the problem only happens when leaving my computer plugged in and idle for a long time, I can disable automatic sleep only when the power adapter is connected, without reducing autonomy.

However, this will increase power consumption and reduce idle time — so you might

To apply this workaround:

• go to System Preferences -> Energy Saver -> Power Adapter tab.
• check the box "Prevent computer from sleeping automatically when the display is off"
• uncheck the boxes "Wake for network access" and "Enable Power Nap while plugged into a power adapter" (I also have disabled Power Nap disabled when on battery, in the Battery tab, but I'm not sure this was required).

*Therefore, some users only reproduce the problem when certain peripherals are plugged in. But for one user it might be Bluetooth, for another one some USB hard disk, and so on — there's no easy to recognize pattern, which might mean the problem is due to whatever driver happens to have an apparently rather common driver bug.

Update: my laptop is a Retina MBP Late 2013, and I am not sure how much this generalizes to other laptop (see comments).