3) In the opponent selection screen in game setup, click on each race in turn and adjust relations. This probably happened to you after playing one of the campaigns-relations don't properly reset afterwards for some reason.
2) Double click on a planet to go into the planet itself, click details, then click governor. You can also get to this screen by selecting a planet on the galaxy map and pressing ctrl+P in TA. Deselect "auto upgrade improvements as they become available". You may also want to deselect "automatically terraform as technology becomes available".
Unfortunately, there's no global toggle for this setting, although it has been requested multiple times. You'll just have to do it on a planet-by-planet basis. What I like to do is set it up when I first colonize a planet, so I don't have to go through them all later on.
1) Honestly, I don't know. I would assume so, but I've never tested it.
Eventually, you'll run out of techs to research, and you'll either have to research what's left, or just turn off your research funding. But after researching each tech, you technically do "stop" researching-you only research one step at a time, although you can get multiple techs due to overflow if your research output is high enough. So, if you don't want to research something, just ignore it.