Why not keep the existing alternator, but wire in a circuit so that it only charges when you're braking? Should be fairly simple, just a relay that's energized by the brake light circuit.
And if you want to get a little more complicated, and have a second switch that lets you turn on charging when you're going downhill or coasting to a stoplight. You could also monitor battery voltage with a Scangauge or similar, and turn on charging if the battery gets critically low...
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