Hello and welcome to DoF!
Love to see well structured posts like this.
1) disappearing unit flags and unit loosing control this is a bug we are hoping to fix with-in a patch or two.
2) is a known issue, which to be honest haven`t been implemented yet as it`s considered a minor feature VS the bigger features like alliance and guilds that we are working on. But down the road we will implement this as well.
3) This is an extremely rare bug which we are working on, not sure if the solution will make it into today`s patch but definitely in the next one.
4) I like your idea about adding a unique flag to the hero - might work out really well actually, I`ll run this by the scritpers. Meanwhile my advise is to make use of the automatically created unit groups in the top-left corner of the screen. Double clicking on them centers view on the unit - and is great for locating and controlling your hero.
5) If you mouse over resources income rate (for example under Food counter, you`ll notice something like +1.5) it`ll provide that information - how much livestock, peasants, buildings e.t.c are adding per minute. But seeing how you haven`t been able to locate this on your own - this gives me an idea to make this pop-up display if player mouse-overs anywhere near the resource counter.