Hi and welcome!
I'll give a shot at a these questions...
1) To mirror a single marking there are a couple of options. A) selecting and copying just that one marking, and copying it to it's own layer, then doing the mirror on that layer B) selecting the marking, and then doing the mirror tool on only the selected area, which should leave the other unselected markings untouched.
2) A very common method is using a brush tool with a decently wide feather, so that a clean gradient forms.
3) If this is for FS2004, then you can control reflectivity with the alpha channel of the repaint. We don't have a specific tutorial on this at present, but I've done it several times so I can discuss it more if you'd like.