Hola, Lionel!
1) On an Action Roll, the GM evaluates all the most significant factors that would grant EDGES for either or both sides.
2) Once an EDGE comes into play, it is determined if that means an increase or decrease of either Threat Level or Effect. There are suggestions on which one depending on the situation on the second internal panel of the GM's guide.
3 A) Once gear or special resistance are depleted, the Runner must find ways to recover it in fiction if they wish to use them again. For example: you deplete your armor when resisting a huge blast and that armor is gone. Later in the run you take the bullet proof vest you find in the trunk of a police vehicle. Now you can mark armor again to resist.
3 B) Following up with the answer above, it's perfectly acceptable to use Flashbacks to produce Gear or other assets that you wouldn't have access otherwise!
4) The penalty incur once you fill in a square for the level. Marking a second Harm on the same level doesn't build up the penalty (a -1D remains at -1D). If you have to mark Harm of a certain level but that level has no spaces left, you must mark the next free level. So yes, if you receive a Level 1 Harm while both Level 1 and 2 are already filled, you suffer a Level 3 Harm instead!
Hopefully I have cleared your doubts, but don't hesitate to ask again if otherwise :)