Welcome to the forum Scarophion.
1. You need a special file called description.ext. It's very easy to use and there are tutorials in the Ed Depot. There is also a template you can use in the Tutorial Mission.
2. Yes, roughly - just reduce the amount of ammo the player has at the start of the mission by reducing the ammo bar. I'm not sure how to do it exactly, since I don't know how to add or remove rounds, only whole magazines.
3. Yes, but to do it exactly would be pretty hard work. (You would have to use getPos and setPos commands on every unit in the Intro/start of mission.) What I suggest it that you control the Intro quite tightly, so that the battle is the same each time. Then you can simply lay out the start of the mission in the same way. Nobody is likely to notice any minor differences such as a body lying in the wrong attitude.
Hope that helps. The questions made perfect sense.