Make sure all your connectors are correct and re seat them a bunch of times. It's highly recommended that you re pin all the connectors in a system 80 machine. It can be quite a job but I think it really helps the long term performance of the machine. Look into the Ground Mod everybody recommends for it. My Mars machine pretty much non functional till I preformed this mod. Also make sure your power supply voltages are correct.
http://www.pinwiki.com/wiki/index.php?title=Gottlieb_System_80
I watched a video from TNT Amusement and Todd said only ground mod you need to do is the one between the driver board and MPU board. Not sure if this true or not it's a easy mod to do though. Just need the crimp tool and pins.
Replace the orange cap above the coin box in the bottom of the cabinet if it's still there.