Great bike for a conversion.
+1 to what Dogman said. Stick the ebrake handles in a box someplace dark. I might make a bike themed coat rack out of all the ones I have around here.
The shifter/brake combo you have will be fine. just add a small space between the throttle and the brake so the shifters clear. Those Acer brake levers are better quality than the ebrake levers
Motorcycles don't kill the motor when you grab the brake, there is no reason an ebike should either, unless you just can't handle the idea of releasing the throttle while grabbing the brake.
as for regen, If you have a DD hub and want it, it's easy enough to ad a button someplace to activate it, or put an inline switch on the cable