Engine jerks

My car was parked near a drainage grate which got blocked so it flooded my car. The foot wells of the car where almost full. The car was not run for about 2 months after that. When we tried to run it, it would jerk badly and every time we tried to break it would stall. We thought it was just dirt in the exhaust or something so we tried to take it for a long drive on the highway. We did check the oil and water before we left. The engine blew. It has been rebuilt, (on the cheap) but it is still extremely jerky and still stalls when you break. If you pick up some speed and start doing like 80km per hour it runs pretty smoothly. What could possibly be wrong?