Yeah, that's why the energy pipes are called 'kinesis pipe' - because they transfer air pressure. Not!
Imho MJ is not rotation or motion either, it's more like vibration. The more energy a pipe transfers the bigger gets the blue line because the amplitude of the vibration rises. Engines produce waves of vibrations which carry forward in the pipes.
Vibration explains best why you can't store MJ and the system looses power over time and the power pipes initially were lossy per section and could explode on overload. You simply cannot store vibrations (try keeping a triangle sound).
Also, the sterling engines do not overheat, the vibrations get too strong if they can't output their energy and its casing bursts.
The only thing I could imagine as a MJ storage is a kind of tube that stores the vibrations and is stimulated in its resonant frequency (which itself would cost energy but far less than stored in the tube). Much like the
http://en.wikipedia.org/wiki/Delay_line_memory in the older days. That would also fit into the philosophy of loss in BC energy - a powered energy storage device.