I am too stupid, please help me out

Yeah the second half lost me too. I found it less and less clear what their intentions and motives were and how it all fit in with what they set out to do in the beginning.

Never even met the Reyes character, that was disappointing. I did like the sign language scene... that's about all I liked.

Sicario 1 far better IMO.

No, you are not stupid. The movie is confusing and English is the only language I know. This is what I think:

1) they 'fake-rescue' the girl.. why this step?
The U.S. didn´t want anyone to realize that they were the ones that actually kidnapped Isabel. With the fake rescue, they can ¨legitimately¨ get the girl into their custody.

2) they wanted to put the girl into some enemy territory? and kill her there?

They wanted to put Isabel deep in rival cartel territory. So Carlos Reyes would wage war against the other cartel.

3) the police escort works for the mafia and shoots the americans - with also the girl there?

The police escort worked for a rival cartel, not for Carlos Reyes. Yes, Isabel was there. the rival cartel wanted to kidnap Isabel.

4) Although the Americans shot back in self-defense against the corrupt police force, this can be seen as an act of war towards Mexico from the Americans. Thus, the Americans did not want any witnesses including Isabel & Alejandro.

This movie was confusing to me. My biggest question is the ending when Alejandro is waiting for Miguel and asks him if he wants to be a sicario and his future.