The twin batteries and external controller for the MPIII is definitely feasible, but there will be a fair amount of wiring that will need to be modified and/or replaced.
The Cycle Analyst itself should not present too much of a problem to carry out the basic installation, but the wiring might be a bit more involved, should you wish to make use of the more advanced features that it is able to offer.
If you have lots of long, steep hills, then overheating could become a problem, but it is most unlikely that you will be using anywhere near maximum current for any real length of time, as the current will quickly diminish as the bike speeds up, and I find my bike speeds up pretty quick with higher amps.
Most of the higher powered Pies on this forum have been either MPIs and MPIIs, rather than MPIIIs, but I see no reason why the MPIII windings should be any less capable of withstanding the higher current.
The more current you put through the motor, the more torque it will develop, so the dropouts
must be capable of withstanding the increased torque. I strongly recommend fitting a pair of strong torque arms if you are going to be using a controller that delivers 40 Amps or more.
The biggest problem I can foresee, apart from the obvious legal implications, is that it may be very difficult to accept riding a low powered bike ever again once you have experienced the impressive power increase that the higher amps will magically produce from your innocent looking Magic Pie.
Having thoroughly enjoyed the acceleration and power that comes with high amps, albeit for a very short duration, I am very keen to have that amount of power available again:
One day, I intend to make it happen again, but I just hope that the power will manage to last a lot longer than it did the last time I experienced it.
Anyway, I'm already thinking about how much wear and tear I'm going to be saving on my front tyre, by simply twisting the throttle and keeping the front wheel off the ground for as long as possible.
Whoever it was that said, "You can have too much of a good thing", obviously wasn't talking about the Magic Pie's power output.
Alan