An interesting experiment you can do Mick is this. Run your fan/monopole as normal and place the negative lead of your multimeter on the negative of the run battery and your positive lead on the positive of the charge battery. You are now reading the sum voltage of both the batteries, abiet a small loss depending on the resistance of your coil and voltage drop over the diode. Nevertheless, once your wheel/fan is up to speed you will notice that not alot of energy is lost. Sometimes, if built properly, you can watch voltage steadily climb

. Helps if you're multimeter can read to two decimal places @ 20+ volts.
Measuring the output of the charged battery in joules however is the most scientific way to prove any sort of unity/overunity effect (I dont like the word overunity) and it is usually marginal, but you must also factor in the mechanical, which, especially in the fans, can be useful/significant. Also remember that the input amperage as shown on your meter isnt totally correct either, it is an average. Remember, we are dealing in pulses here. A more accurate way is to measure MPPM and go from there. The SG groups explain this part of the testing quite well.
Using the ignition coil you must remember one thing. The secondary is directly connected to the primary, and while there is high resistance on the secondary, this direct connection can be undesireable for certain configurations.
In regards to a motor I think you should ask yourself what it is exactly you want from a larger motor. It sounds to me like an energizer could be a handy tool to have in your part of the world, with alot of batteries lying around. Any if you choose to you can make one that is quite powerful and will recover/charge much larger batteries, along with some mechanical, alot faster than your fan ever will.
But if you are primarily after torque and a motor function then there are other designs that may be more profitable to pursue. I wouldnt bother with building a motor with the intent of attaching a conventional generator/alternator to it, in the hope of short circuiting one into the other, Im sure youve seen that none of these machines run in a constant closed loop. So saying, there is merit in harnessing/capturing the rotating magnetic field, you just have to be clever about how you do it. So an unconventional generator/alternator attached/integrated isnt out of the question either.
The main problem you may face is simply construction and access to machining services and parts if you chose this route. Trust me, you want to make sure that the rotor is secure, balanced and safe. The window motor I recently built I now have to tear apart, the thing is just an animal. I endeavoured to make it as balanced and true as possible, but it all goes to hell over 1000rpm. Awesome machine, but just not safe in its present configuration. Ive learnt a few things since and if I build it again its going to be a machined rotor and thicker shaft with solid bearings and frame work. And multi coil too. But thats a whole different kettle of fish.