that would be to place the capacitors in parallel with the battery pack. have a way that on initial takeof the vehicle draw from the ucaps. when the crusing speed is reached, the batteries are put in and the ucaps taken out. the ucaps are then filled up by the batteries through a controller that would only allow 200 amps to go from the batteries to the ucaps.
You would likely be better off to simply keep the capacitors in parallel with the batteries all the time. This would essentially give you two parallel current sources, one with much lower impedance than the other.
Let's look for a minute at the actual storage capacity of your capacitors:
3000F/60 = 50F Total Series Capacitance
60 * 2.7V = 162V Maximum
Assuming you still want to use 12V lead-acid batteries,
162V/14.4V = 11.25 ==> 11 * 14.4V = 158V Nominal System Voltage.
The capacitors will be able to store:
1/2 * 50F * 158V^2 = 624,100 Joules of energy when charged to nominal system voltage. There are 3,600,000 Joules in 1kWh.
Your 210Ah lead acid batteries should not be discharged past 50%, so you will have a nominal 105Ah of usable current @ ~14.4V, or optimistically, 1.5kWh of power. If we assume each of your batteries are capable of ~640A, then this implies an internal resistance of ~ 0.25 ohms ( 158V/640A = 0.247865). 11 of these batteries in series gives you a total internal impedance of 11 * 0.25 = ~2.7 ohms. So, your series connected batteries should have a maximum current of 158V/2.7ohms = ~58A.
A 250A load @ 158V implies a load resistance of 0.632 ohms. Assuming you were "running" on the 50F capacitor bank alone, initially charged to 158V, you would initially provide 250A to the load. 1 second later, you would be supplying only 182A, and the capacitor voltage would be 115Vdc. @ 2 seconds you would be supplying 133A @ 84V.
Designing a viable electric vehicle requires engineering the entire vehicle from the ground up. "Adding" a 15kW generator (typically a 25hp to 30hp ICE) pretty much defeats the purpose. In any case, I can't see how these capacitors are going to do you much good as a primary storage media, they may be of some use for a second or so, but not a lot else.
As far as using multiple PWM controllers, the simple answer is "no". You could use multiple units if you were willing to separate the capacitors into "charging groups", and then "switch them back" to a single series, but this has its own problems that I won't go into because I think the entire way you are attempting to use the capacitors is flawed.
Good Luck!
Fish