2004 Saturn L300 car sputters and idlrs low

The thermostat on a 2004 Saturn L 300 the upper and lower intake manifold to reach the thermostat I'm not a mechanic and it took me two days to take it apart and put it back together I lost some of the bolts from the intake manifold and when I started the car it hesitated and died at first after I removed the intake manifold again I found lines were not connected properly I connected the lines and now the car stays running and it didn't at first but it idles low and sputtered I don't know what I did wrong please help. Also I broke a connector on a valve THAT is hooked up to a black box with a blue line going to it