I am not sure about XP distribution from surveys. I only use fleets on the defendant anomaly so the XPS actually come from the battle. Those regular survey ships are vulnerable what I do is clear and entire sector militarily first then send all my surveys ships at once using the commands menu.
I think the research does affect everything in the last game people got real tired of all those individual upgrades.
I'm still not sure about your third question but I'll look into it
Each ship has a number of options for upgrade and you can find all of them in the commands menu. Most lateral upgrades to other ships of the same size are available.
Planetary invasion can be found faster. Clicking The hourglass in the upper right of the research menu will bring up four options click military to get military specific tech offers. Read the leads to at the bottom of every tech. The one before planetary invasions is something weird that you wouldn't expect can't quite remember.
Basically every world would be slightly more efficient with a governor. But governors are expensive so it may not pay off. I never put a governor on below class 3. When I was playing the giant map I only did class 10. It's a player preference based on how annoying you consider micromanaging too many worlds to be, and how many governors your society can afford.
Spreading quickly has a lot of advantages. Just make sure you don't spread so quickly that you can't defend your own terrain. Also make sure not to cripple your food management or economy in the process of spreading. Every time you colonize a planet that's one food spent, it could also bring food back just pay attention to the details.