What are the percentages above the alien icon

Aim and Defense are pretty simple. As you suggest, they're simply lacking a % sign.

Aim is your base chance to hit. A rookie's starting 65% Aim means a 65% chance to hit.

Defense is also pretty simple: 10 Defense means 10% less chance to hit.

In this way, you can think of Cover as providing Defense, and standing in a smoke cloud makes you 20% less likely to be hit, hence, 20 Defense. (Incidentally, 65% base Aim and -20% for low cover is why most Rookies have a 45% chance to hit sectoids in your first couple of missions).

Additionally (thought not a stat per se), different weapons get different range bonuses, which increase or decrease your chance to hit. Shotguns can get up to 37% bonus chance to hit at point blank, and Sniper Rifles actually get a penalty if you're too close.

It means you just flanked an alien. If you notice the shield next to their name showing how much cover they are behind is also yellow. Also if you notice, when your soldiers are flanked, they have a yellow shield icon as well.

Thus far, I have only encountered yellow and red.