How do I flash two joining peaks of different heights?
You could flash it with 2 pieces of sheet lead, which will stretch enough to feather with sufficient overlap.   

You could do the same with sheet copper. It would probably tear a bit, but then solder a small patch over the small tear.

With either copper or lead, you can do it with one piece by folding the sheet onto itself creating a z-fold yielding a triple layer. Start by laying it up the back side of the small gable, then up the rake board, then flat onto the main roof. Then start the z-fold on what will become the lower edge that spans the small gable and onto the main roof. Once formed, you'll want to install it under the rake board.  To help see how to do this, form it first with a rectangular piece of cloth, such as a bath towel.

The valley formed by the two lower gables will also need special attention. Cut a narrow triangular piece of sheathing to sit in the valley to create a sloped floor on the valley (that slopes away from the upper gable's wall).  From the looks of it, the isosceles triangle would be 4-6 inches across the base, and 18" long (high).  The porpuse if the triangle sheathing is to support the flashing.  Sheet flashing with z-folds will work there too.