1) It's just a port over from Diplomacy so there should be lots of these types of issues due to new damage and armor types, as well as adjusted values for entities not covered by DS compared to those that are adjusted by DS. By that I mean, the entities that the mod doesn't overwrite are using new finely tuned values that had months of internal and external Alpha feedback to tweak, whereas the entities that are included in DS are just now getting those. If you have any specific issues, such as an upgrade to an ability that actually makes it weaker instead of stronger for example, PM Ryat or Carbon directly or use the mod's underutilized bug report link http://distantstars.mmobase.com/?m=reportabug stating which ability to get the issue addressed before the next release. Don't just assume stuff you find will be taken care of in the next release because you might be doing something that the team testers are not doing and thus they won't know about it.
2) It's probably an issue with the grav well radius and hyperspace radius exit values recorded in a few new places. As far as I know, all of the values for the planets are the same. Probably just a simple adjustment needed on the gas giant side of things.
3) Could be tech related, could be an issue with the core game. When they are massed up and waiting to jump, I assume you have their phase jump toggled to 'All Grouped'. Does this behavior persist when the toggle is switched to 'None Grouped' when they're all lined up trying to jump? If it doesn't, it could be that the group is waiting for a ship to line up that can't move past others in its way that are waiting for formation.
4) Diplomacy had issues with there being far too many pirates going on these raids. Due to this being a port over from Diplomacy, it's likely that the raid values are far too small to support the type of raids we all know and love. Ryat will adjust this especially when he gets around to updating Powerful Pirates to work properly with Rebellion. He won't tolerate his little ones being treated in such a manner for too long.
*Edit* Upon further review of #2 with someone else doing what I told them to do, the issue is from the new radius values included in the map files themselves. They overwrite what is included in the entity files. I updated all of the maps with the values I found somewhere so they are all identical for all planets, whereas the entity files have different numbers.
These are the values I used for testing and the test subject seemed happy with them:
R is the move radius, E is the hyperspace exit radius.
Star R 90000 E 90000
Companion Star R 50000 E 50000
Gas Giant R 80000 E 75000
Gas Dwarf R 70000 E 60000
Huge R 45000 E 37000
Normal/Home R 40000 E 33000
Dwarf/Wormhole R 35000 E 29000
moon R 30000 E 25000
Asteroid R 20000 E 17000
belt/junk/anomaly R 15000 E 15000