Rebuild transmission troubles

Did you take the valve body apart to clean it? If so did you get the manual valve (the valve that the shift linkage moves) correctly located so it moves when you move the shifter?

When you bolted the trans up to the engine and then proceeded to bolt the torque converter up to the flex plate did the converter spin freely? Did you have to pull it forward a little to meet up with the flexplate?

Are you checking the fluid in neutral? If not you should be