A Charnley,
I think your whole plan has a flaw. (another one)
Compare Super Cap to a Battery.
1) Pretend we have a 5V battery. Likely it will have a voltage of 4.75V at 10% charge and 5.25V at 90%. You can run the USB directly off the battery. Just like your project states.
2) A capacitor stores energy by CxVxV. Capacity times Voltage squared. 4.75^2 =22 while 5.24^2 =27 With a capacitor, you will charge until you have 27 unites if power, then discharge down to 22, then back up to 27. So the ability to store (and use) is from 22 to 27.
x) Battery can store from 10 to 90 while the cap is storing from 22 to 27. Most of the cap is not used.
I think the dynamo needs to be run where it works best.
AND
The capacitor needs to have a very large voltage swing, to store more power.
Over at Linear.com they have some examples where they charge up a cap to (any voltage) then use a PWM to regulate to get 5.0V out.
Example: Capacitor = 10V. Output is 5V for USB. Then use a "buck/boost" PWM to take any voltage from 3V to 10V and make 5V. Now the capacitor voltage can range from 3V to 10V. (V squared = 9VV to 100VV) Now you can store and use power from 9 to 100 units. The ratio of 9:100 is much larger than 22:27. (and the output is 5.0V at full charge and at minimal charge)
My point is use a battery, or battery + PWM OR use a capacitor (with a large voltage swing) + PWM.
I reread and I was not clear: The way you have things use a battery not a cap. Use a cap with a very large swing from Vmin to Vmax, then regulate to 5.0V.