The project you've described would not be too
difficult to implement.  Ideally you'd want the
alternator output voltage to be much greater
than what the DC motor would require.

The capacitor bank would be charged to some
relatively high voltage by rectifying the alternator
AC output into DC pulses.

Then the capacitor bank stored energy would be
applied to a DC to DC Converter to down-convert
the high voltage to the lower voltage required by
the motor.

When the capacitor stored energy is exhausted,
re-charge the capacitor bank and repeat the
motor run time.

It would be very helpful to know what your
intended voltages are; for both the capacitors
and for the motor.  What sort of power level
the motor needs to operate at and the desired
amount of run time.

DC to DC converters for down-conversion
(Buck Regulators) are now available which
can function well over a wide range of input
voltage to efficiently accommodate a declining
capacitor bank voltage input while maintaining a
steady output.  Provided of course that the
capacitor bank is sufficiently large.