I've gotten to this thread late, but I would have suggested making a little cardboard triangle that represents the angle of the notch to the caliper pad slides so you could align the pistons correctly upon re-installation.

At any rate, if you are trying to install the pistons with the heat shields still on, I don't see how you are going to fully seat the dust boot that resides underneath it. Of course, Mercedes makes a special/expensive tool for seating the dust boot, but I was able to do it with patience, finger tips, and a soft piece of whittled wooden dowel. Be careful you don't push too hard with something too sharp as it is easy to tear the thin rubber when it is pushed too hard against the brass retaining ring inside the boot.

You may be better off just removing the heat shield, installing the piston correctly, fully seating the dust boot, then re-installing the heat shield. Mercedes makes a tool for this, as well, but most of us just carefully seat it slightly below the face of the piston. There is a spec for this distance, but I disremember what it is. There are some good threads on caliper rebuilding that should contain the value. It's in the FSM, as well.

Added: I am sure that each piston is the same size. If not, there would have been a left and right version of the seals in the rebuild kit.