Glad you are getting the hang of it, it takes a few runs sometimes for it to click - your brain, not the camera shutter .

Don't worry about the AI they are just along for support. When you are getting near target, you need to come out of autopilot if you are using it and fly directly to the target waypoint. In flight, you can bring up the map (M) and check the altitude in there too. Just climb to that altitude. There is a slight leeway, so it doesn't have to be exact, but best to try your best to be as close as possible for maximum chance of a good photo or recon.

Check the map. Look at the first waypoint over the lines - zoom map to max will help (cycle with key combination Control Shift M).. Fly over the first waypoint and when you think you are in the middle area do your recon thing, photo etc.
Depends on weather settings too, make sure you have bad weather affects missions ON in Workshops otherwise you may get to do photo recon at low altitude in poor vis, which won't work!

The mission replay is your last mission so if you fly QC you would lose a previous recording.