I would leave the alternator alone. Lots of engineering and carefully considered decisions went into its design. Nothing good will come out of trying to "rewind" it. You're just going to mess it up.
Either get the right generator for what you are trying to do, or deal with the output of this one. Modern electronic switching power supplies can do pretty efficient conversions. Think of a switcher as a electronic gearbox, just a lot smaller, cheaper, lighter, less messy, and with no parts to wear out.
If you really want to get fancy, you do power factor control on each of the three outputs separately. This will cause the input torque to be smooth over the whole rotation cycle. However, even just rectifying the three phases and then dealing with the resulting DC should still get you where you want to be.