It's a solid concept, in fact you could almost turn the car into a mild hybrid. You could easily wire a relay to the brake switch so that when you stepped on the brake the alternator would go into full charging mode. I picked up an idea for my Civic hybrid from another member here to wire up a switch to disable both charging and regen, then add a relay that overrides the switch when the brake is applied, so it will always regen on braking. The idea is to never have forced regen (IE while driving) by only using as much assist as can be provided for by regenerative braking.
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