First is the rate at which you can generate the precursors. How many can you generate in a picosecond? That's how big your explosion can be. Or rather, the explosion will be as big as how many you can generate in a picosecond, times however many picoseconds you can sustain generating them (plus the force needed to make the fusion reaction happen).

The second problem is that generating the ingredients probably takes at least as much energy as you get out of the fusion reaction. At that point, whatever you're using to generate the energy can be your weapon, without needing the intermediate step of the quark fusion reaction. (As the Schlock Mercenary web comic says, "Any sufficiently advanced technology is indistinguishable from a really big gun.")