Realistically, the only topology usable at such power levels is a Full Bridge or a variant thereof like a Phase Shift ZVT. Indeed, common recommendations are <100W for a flyback and full bridge should be used at >500W.
There are two reasons for this. First, both boost and flyback operate using energy storage. That means you charge up a magnetic field from the input and then dump that energy in to the output. Obviously, then, the power is limited by how much energy the magnetics can store and how quickly it can charge/discharge. The second reason is that the full bridge topology is the only one that fully and evenly utilizes its components. Others will add additional stresses on the switches and/or only partially use the magnetics. For example, in a boost converter the switch must be able to handle both the low-side current and the high-side voltage. Additionally, the inductor is only ever charged one way, meaning it must operate from one side of its hysteresis curve to saturation. At low powers, such inefficiencies aren't a big deal. At higher powers, however, they makes things difficult if not impossible.
Anyways, a multi-kilowatt power supply is not for the faint of heart. It requires a lot of design work and has lots of traps for young players, as Dave would say. It you go this route, you'll need to do a lot of learning, be it via app notes or a book. Generally magnetic companies will be a good source of the former.
Here is one I pulled up after a quick search that looks like a good place to start.
For this application there are other options, however. The easiest, and more efficient besides, way would be to forget the SMPS and just stack batteries until you have >400V and then charge the caps directly from that. (Well, probably not directly and instead via a current limiting PWM, but that's a fairly simply design.) You won't need 3kW batteries then either, as each would only need to handle its own share of the power.
If that's not an option, you can boost it a little with a voltage multiplier / charge pump. They aren't good at regulated power handling, but since you're just charging a capacitor bank they would actually work fairly easily and efficiently. Still, you will
need to start with 4x 22.2V batteries. By boosting the initial voltage, you can cut back on the number of stages and ripple current within each stage to something reasonable.
Ultimately, handling kilowatts is neither cheap nor easy. You will definitely need to decide what your budget is in both effort and money before you know what exactly 'possible' means for charging your caps 'as fast as possible'. My recommendation, however, would be to start with a 100-200W push-pull converter to give yourself an idea of what you're getting into. It should be fairly simple and be able to use a modest sized scrap ferrite core without too many issues.