1966 Ford Galaxie Installed rebuilt 302 V8 motor

Since install car has not run. Rough idling, hard start had to take out performance cam bought from JEG they didnt recommend changing hydraulic lifters which subsequently were damaged. Replaced stock cam except not sure what year rebuilt motor was. Had MSD ignition with computer, performance intake manifold and electronic ignition with high performance four barrel cam. Runs rough will die when get into drive have transmission rebuilt without noticable change. 2 cylinders on each side have intake valves open when should be closed and after turned cam 180 degrees now the problem has shifted to to different cylinders on each side which were working fine prior to cam 180 degree change. Need help with diagnosis.