To avoid getting hit by tracker jackers when the ones come that fly horizontally, jump up or down to avoid them (depending on what part of the stage you are at the time).
When the tracker jackers inside the blue diamonds appear in the corners of the screen and start shooting at you, simply jump up and down to avoid the shots. Don't shoot them. The longer you go without shooting them they stay on the stage for quite a long time and their shots come slowly so they are easy to avoid. This will allow you to build massive amounts of speed to reach the end of the stage.
Stage two: District twelve hints
Shoot arrows at the hovercraft as rapidly as possible while avoiding them.