Prius makes loud thumping noise and won't drive at low speeds or at all.

I have a 2002 prius with 205,000 miles on it. I was having battery issues until i installed a Optima battery and Retrofitted it into the car. Now I have great power but the car bucks and stalls at crawling speeds, even when I towed it back to my house it would do the same thing slowing down or speeding up at low speeds. Any input would be appreciated.