And my other thought on this is that perhaps running it off of the ignition pickup which is pulsed it would only be compressing the air fuel mixture when the piston is about to come on a down stroke so as not to over pressurise the crank and blow the seals
Not to say that an electrical supercharger won't work, because it will work.
But you seem to have a massive misunderstanding of the energies and time lags involved.
There is a massive difference between the energy needed to make a spark and the energy needed to run a supercharger.
Yes it is possible to surround the flywheel with cores and windings and generate enough energy to light the lights and charge the battery and some small bikes do this.
You may still have an order of magnitude less energy available than needed to run a supercharger.
It may still be possible to use the flywheel to generate enough energy to run a super charger, but your flywheel most likely has one embedded permanent magnet. You will probably need about five more embedded magnets.
Do you have the machining skills to add magnets, not to mention the space.
Then you will have to surround the modified flywheel with laminated cores and windings.
On a budget of both dollars and skills, consider a battery driven supercharger for occasional use.
when cruising at low engine power levels, you may use the supercharger motor in regenerative mode and charge the oversized battery.
Then the supercharger may be kicked in to boost for short spurts of power.
Your concerns of pressure peaks at TDC.
Think about the dynamics.
The time required for the supercharger to spool up and develop a pressure spike will be many orders of magnitude greater than the short part of one cycle as the piston passes TDC.
And, as the piston travels upwards, the supercharger is delivering air to an expanding volume.
Past top dead center, as the piston descends, the reeds close and the supercharger is deadheaded.
The crankcase pressure increases without any input from the supercharger and peaks just as the port starts to open.
Think battery powered supercharger and we will look at ways to boost the charging circuit capacity.
How is the battery charged now?
ps; Battery power will probably give you the low end boost that need for wheelies.
Powering the supercharger from a generating circuit will have too much lag for much takeoff boost.
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Ohm's law
Not just a good idea;
It's the LAW!