I replaced my altnator and desconected my batterie now my engine runs rough at

try driving for approx 10 mins and see if all starts to function properly

No its most likely caused to a bad wireing harness my olds was having the same problem I barley got it home but how we fixed it is we had to replace the main wireing harness to the sensors because the wires would glue and cause a short to ground and also their was noise in the line causing a short to ground and the computer couldn't handle it also check for the coil pack the coils or the brain in the coil pack go bad it was a common problem for these oldsmobiles