acedovick;
I had to re-read your questions and information a couple times today to try and get an idea of what you're trying to do:--)
Must be a lack of coffee or that it's Friday, something:--).
Here's what I think you're trying to do and what the possible solutions could be.
The hub motors are very nice to add to exisiting bikes, however unless you get a fraily large one they aren't very good starting from a dead stop, just not enough torque to really get going without really using down the batteries.
A couple questions:
The hub motors you're going to be using ? do you have the control circuitry for them?
Some of these have regenerative circuits in them that will go a long way to doing what you're wanting to do.
Are you also going to have some other energy storage device other than the flywheel? i.e. Supercaps or battery?
Circuits can be built to do what you're wanting to do, and the circuits for the hub motors and the Hieztmann<-sp? add-on motors and controllers thave this already built in, they don't kick the motor in until a certain speed is attained by the pedler.
Some of the things you might want to look at is weight. The flywheel and generator may exceed the safety of the bike ( not so much of a problem if this is a trike or quad).
Is it possible for you to post pictures of the generator and flywheel?
How good are you at mechanics? moving the gearing from the back wheel to the middle is not a trask to be undertaken by a novice. You'll need mig/tig welding abilities and certainly a drill press with highspeed high tinsil strength bits to be able to mount the stuff, plus the flywheel will need to be both statically and dynamically balanced to keep it from making the bike shake uncontrolably at the high rate of revs you'll need to keep the gens at power-producing levels.
Hope some of this helps and do upload pics if possible of all parts involved so we can help as much as possible.
Bruce S