1997 Pontiac Sunfire down a cylinder

Ok I had to replace my engine recently due to not so smart people dropping it from 5th to 3rd. Anyway everything was running fine untill on my way back from picking someone up the oil light came on the the car died we got it started again with a lot of hesitation. As soon as we started the car the temp gauge skyrocketed so we then pulled over and shut off the car well needless to say we were leaking water and the engine was heating up we fixed those problems by changing the thermostat and replacing the thermo housing off the block but the car does not overheat any more but still acts like it is down a cylinder could it be a vaccum sensor or another sensor or something more severe