Mine is a a custom wind too. No, it does not affect the lift, you are just flipping the top plate. But hey, don't worry about it, you are not using the shock bolt/studs and the mounting hole for your shock does not change. I love the regen, so far, I had it set to not lock up the rear wheels on snow but still slow you down. I hardly use the brakes. Only to stop in close quarters or to change direction quickly. The fact that it charges the batteries [up to 40a for a second or 2] does little for the "big picture" in the country.
Drives like my farm tractors, let off the throttle and you slow down. Mode one, [low speed] boosts the torque too. But this is my first cart so I have no experience with hot series motors so maybe I'm missing something there too.