American Flyer prewar - What is this Engine.

That appears to be something that someone has extensively customized/modified.

The pilot and headlight area appears to be modified, as the headlight should stick out of the center, where you indicate the PRR logo is and the pilot is not original American Flyer.  As the original pilots are easily broken if dropped, I am guessing that someone has replaced the original pilot with the present pilot. 

The trailing trucks are not American Flyer.

The manual reverse appears to be a modified original to a c. 1932 3307-3308 engine, and I believe that is what the motor originally began its life as; however, without being able to see the underside of the motor or the motor removed from the boiler, I really cannot say what has been done to the motor or if the motor frame is correct.

The triangular projection at the rear of the cab is correct.

NWL

Well, you have a bunch of parts that were put together.  The 1 front driver looks like it came from a Gilbert O engine, not a Chicago Flyer engine you have. The separate switch assembly is from a different engine, it turned on/off an electric bell. That engine never had one. Not the original trailing truck. It had a 2 wheel pilot truck. Front pilot has been replaced, and where the PRR plate is was the headlight opening. The top headlight is not original. You have a early boiler shell stuck on a later chassis.

The original Flyer engine would have looked something like this

  Since your engine amounts to an extensive kitbash it might be worth trying to bring it back to life - based on the pictures it looks like the biggest issue would be acceptable new drivers but if that can be overcome and it can be made to run again it would make for a unique piece of rolling stock.