I don't think you can cram more fuel in than will fit there, without pressurizing it. If HHO has 3 times the energy density of petrol/air mixture at the same pressure then all you can do it put the same volume in and get 3 times the energy out. Of course you're also putting 3 times the energy in so it's not necessarily improving efficiency.

No need to slow it down to match the HHO generator. Just use a faster HHO generator, or a bunch of slow ones.

It still works the same if you consider it as a continuous process that just consumes x liters of fuel per second, without breaking it down into individual strokes. You could actually make it a more continuous process by having more cylinders and/or some buffer reservoir for the fuel.