1. You can make notes via the system report. Right click on a sector and you'll see a system report option at the bottom of the list.
2. I've seen this from time to time, not sure what causes it. It's sort of random and will only effect certain planets.
3. Sometimes the internal design type (used by the AI) doesn't match a player's design type. Updating to v1.14a should fix it.
4. You can use PBW for non-hotseat play. Here's a link that explains how it works:
http://www.pbw.cc/text/faq.jsp