Engine shake

After coming to a stop, the engine can sometimes shake very hard, in fact, it makes the steering wheel vibrate. But if you put it into neutral, it will smooth out and stay that way when you put it back into drive, until you come to a stop again. When you put it into reverse, it will also shake then as well. The trans was just recently rebuilt and a new converter put in. The trans shifts perfectly, no slippage or weird noises. There are no codes for the trans, just the IAT on the engine side of things. The main motor mounts were replaced when the valve job and timing belt work was done. The injectors were removed and cleaned, tested for spray pattern and all are fine. Plug wires are almost new silicone rubber ones, plugs are new.