I have had instances where when you put the new linkage on. They have to be factory specs. You can transmissions where the linkage is different even though the transmission is the exact same. As for the shifter you must make sure the linkage inside is all set correctly. The reason being is the actual throw of the linkage may not be correct and trans will not go into gear correctly. Do you have park and reverse? Try getting under the car and disconnecting the linkage. Then get another person and some blocks. This could be dangerous if your retarded. Push the throw at the trans where the linkage would hook up. Push it into drive and see if it goes through gears correctly. You could also put the car on four stands this would make it easier. The point is try driving without the linkage. If the trans goes through gears correctly then you know its somewhere in the linkage.
I have taken these issues to transmission shops and the a hole tells me he wont even touch it because it doesn't have the linkage that came with the car and trans. Meaning if it wasn't stock he would not install a new one. He would only sell me one.
I HOPE WE ARE TALKING ABOUT A TRANS THAT IS IN GOOD WORKING ORDER!