[Suicide Junkie]

1) 100M people gives a 5% bonus.
500M gives 10%
1Billion gives 20%
every billion after gives 10% more than the Last
8 billion gives 90% bonus
10 billion gives 100% bonus

2) Ruins will give one of two things:
1 to 5 random, regular tech levels.
1 of the unique ruins tech (planetary shields, massive weapons, Neural combat net, etc)

If you have already got what the ruins would have given you, it will not show up in your log.

Some mods also add "dummy" ruins that do not actually give anything useful.

3) Cloaking is strategic-only. If a cloaked ship is in the same sector as a battle, it will be seen, and join the battle.
Cloaking also drains supplies, and takes up space that could be used for weapons and shields.
There are sensors available to research that will render cloaking (of an equal or lower level) useless.
At max tech, the sensors beat the cloaks.

4) There is a "fleet" button in the command bar. The icon is of a group of ships, with a Plus sign in the corner.
Select a ship, click that fleet button, "Create Fleet", then click to move ships into it.
If you exit that window and select the fleet, you can give orders to the entire group of ships at once, and set their common strategy with the "chess pawn" icon in the command bar.

5) See 4.
You need to set strategies before combat happens. If you are doing "tactical combat" with manual control over the ships, you can set the formation when you designate the leader.